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MBD4
Final classification
VUS
MBD4 c.1382A>G · p.Asn461Ser
MBD4

MBD4 NM_001276270.2:c.1382A>G (p.Asn461Ser) is a missense variant in exon 5 encoding a non-conservative amino acid substitution from asparagine to serine at codon 461.

Gene
MBD4
Transcript
NM_001276270.2
HGVS · transcript:coding
NM_001276270.2:c.1382A>G
Consequence
N/A
GRCh38
chr3:129433861 T>C
GRCh37
chr3:129152704 T>C
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: BP4 supporting; combination = 1 supporting benign, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: BP4 supporting; combination = 1 supporting benign, which maps to VUS.
Classification rationale
BP4 VUS
MBD4 c.1382A>G

MBD4 NM_001276270.2:c.1382A>G (p.Asn461Ser) is a missense variant in exon 5 encoding a non-conservative amino acid substitution from asparagine to serine at codon 461. This variant is present in gnomAD v4.1 at an allele frequency of 0.202% (3,262/1,614,054 alleles, including 8 homozygotes) and in gnomAD v2.1 at 0.169% (479/282,746 alleles, including 2 homozygotes), indicating it is not a rare variant in the general population.1 Multiple lines of in silico evidence suggest no significant impact on the gene product: BayesDel scores -0.063 (benign) and SpliceAI predicts no splicing impact (max delta score 0.15). REVEL scores 0.54 (borderline deleterious) but does not overcome the preponderance of benign computational evidence (BP4 supporting).2 No variant-specific functional studies, segregation data, de novo observations, or case-control studies were identified in the literature or ClinVar submissions.3 ClinVar classifies this variant as Likely benign based on submissions from multiple clinical laboratories (4 Likely benign, 2 Uncertain significance), though the aggregate review status remains single-submitter level.4 Overall, the only criterion met is BP4 at supporting strength. No pathogenic criteria are met. Insufficient evidence exists to classify this variant as either pathogenic or likely pathogenic; the classification is Uncertain Significance (VUS). The population frequency data and clinical laboratory consensus lean toward a benign interpretation but do not meet formal benign classification thresholds.

BP4 VUS
Gene diagram · NM_001276270.2 · variants mapped to exon structure
MBD4 NM_001276270.2
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 19 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
BP4 supporting Benign
Multiple lines of computational evidence suggest no significant impact on the gene product. BayesDel scores -0.063 (benign) and SpliceAI predicts no splicing impact (max delta = 0.15). While REVEL scores 0.54 (borderline deleterious), the preponderance of in silico tools (2 of 3) supports a benign interpretation.
BayesDel = -0.063 (benign)SpliceAI max delta = 0.15 (no splice impact). REVEL = 0.54 conflicts but does not override the two benign-supporting tools.
Assessed · not applied
Pathogenic
PS1 No alternative nucleotide change at c.1382 has been reported as pathogenic.
PS2 No de novo data are available for this variant.
PS3 No variant-specific functional studies were identified.
PS4 No case-control or statistical evidence demonstrates enrichment of this variant in affected individuals.
PM1 The variant (p.Asn461Ser) is not located in a statistically significant mutational hotspot (cancerhotspots.org analysis negative) and no well-characterized critical functional domain specific to this residue position was identified.
PM2 This variant is present in gnomAD v2.1 at AF = 0.169% (479/282,746 alleles, 2 homozygotes) and in gnomAD v4.1 at AF = 0.202% (3,262/1,614,054 alleles, 8 homozygotes).
PP1 No segregation data are available for this variant.
PP2 No gene-level constraint metrics (e.g., missense Z-score, missense o/e ratio) were available for MBD4 to establish a low rate of benign missense variation.
PP3 In silico predictors are conflicting.
PP5 ClinVar classifies this variant as Likely benign (not Pathogenic) with a review status of 'criteria provided, single submitter' (1-star).
Benign
BA1 gnomAD v4.1 allele frequency is 0.202% (v2.1: 0.169%), well below the 1% BA1 threshold for a benign common variant.
BS1 gnomAD v2.1 AF = 0.169% (grpmax FAF = 0.254%) and v4.1 AF = 0.202% (grpmax FAF = 0.236%).
BS2 While gnomAD reports homozygotes for this variant (2 in v2.1, 8 in v4.1), there is no confirmation that these individuals are healthy adults, which is required for BS2.
BS3 No well-established functional studies demonstrate that this variant has no deleterious effect.
BS4 No segregation data are available demonstrating lack of cosegregation with disease.
BP1 MBD4 is not a gene for which primarily truncating variants are known to cause disease.
BP2 No data are available demonstrating that this variant has been observed in trans with a pathogenic variant in MBD4 (for a recessive disorder) or in cis with a known pathogenic variant.
BP5 No case has been reported in which this variant was observed together with an alternate molecular basis for disease in the same individual.
BP6 ClinVar review status for Variation ID 1336001 is 'criteria provided, single submitter' (1-star), not 3-star expert panel.
N/A · 5 PVS1 · PM5 · PM6 · PP4 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 0.002021; MAF= 0.20210%, 3262/1614054 alleles, homozygotes = 8) and has highest observed frequency in the European (Finnish) population (AF= 0.00317148; MAF= 0.31715%, 203/64008 alleles, homozygotes = 2); grpmax FAF= 0.00235897.
v2.1
This variant is present in gnomAD v2.1 (AF= 0.0016941; MAF= 0.16941%, 479/282746 alleles, homozygotes = 2) and has highest observed frequency in the European (Finnish) population (AF= 0.00310658; MAF= 0.31066%, 78/25108 alleles, homozygotes = 0); grpmax FAF= 0.0025446.
🇨🇦 CA
This variant is present in gnomAD-Canada v1.0 (AF= 0.001628841350852427, 30/18418 alleles, homozygotes = 0).
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.2% · 3262 / 1,614,054
8 hom · FAF 0.24%
European (Finnish)
203 / 64,008
0.32%
2 hom
European (non-Finnish)
2872 / 1,179,952
0.24%
6 hom
Remaining individuals
101 / 62,510
0.16%
Ashkenazi Jewish
28 / 29,602
0.095%
African/African American
30 / 75,036
0.04%
South Asian
19 / 91,078
0.021%
Admixed American
9 / 60,016
0.015%
+ 3 not observed (Amish, East Asian, Middle Eastern)
gnomAD v2.1
0.17% · 479 / 282,746
2 hom · FAF 0.25%
European (Finnish)
78 / 25,108
0.31%
European (non-Finnish)
349 / 129,084
0.27%
2 hom
Remaining individuals
18 / 7,216
0.25%
Ashkenazi Jewish
10 / 10,364
0.096%
African/African American
13 / 24,964
0.052%
South Asian
6 / 30,616
0.02%
Admixed American
5 / 35,440
0.014%
+ 1 not observed (East Asian)
gnomAD Canada 🇨🇦
0.16% · 30 / 18,418
0 hom · FAF 0.098%
Latino/Admixed American
3 / 836
0.36%
European (non-Finnish)
26 / 11,740
0.22%
Ashkenazi Jewish
1 / 832
0.12%
+ 6 not observed (African/African American, East Asian, European (Finnish), Middle Eastern, Remaining individuals, South Asian)
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar as Likely benign (4 clinical laboratories) and as Uncertain significance (2 clinical laboratories) and as Likely Benign (1 clinical laboratory). (ClinVarID = 1336001)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.15). REVEL score = 0.54. BayesDel score = -0.0631527.
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. MBD4, a DNA glycosylase, is infrequently altered in cancer.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 7 PMIDs not cited in assessment
25626707 ↗ Whole-genome sequencing in newborn screening? A statement on the continued importance of targeted approaches in newborn screening programmes. CLINVAR
25730230 ↗ Expanded carrier screening in reproductive medicine-points to consider: a joint statement of the American College of Medical Genetics and Genomics, American College of Obstetricians and Gynecologists, National Society of Genetic Counselors, Perinatal Quality Foundation, and Society for Maternal-Fetal Medicine. CLINVAR
25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
23037933 ↗ Including the initial newborn screening bloodspot collection device serial number on birth certificates: basis and recommendations from the Secretary of Health and Human Services' Advisory Committee on Heritable Disorders in Newborns and Children. CLINVAR
23881473 ↗ Newborn screening: education, consent, and the residual blood spot. The position of the national society of genetic counselors. CLINVAR
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR
31022120 ↗ ACOG Committee Opinion No. 778 Summary: Newborn Screening and the Role of the Obstetrician-Gynecologist. CLINVAR