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NM_014915.2:c.-140C>G
p.? · ANKRD26
ACMG/AMP
0%
complete
Final classification
Benign
BA1BS1
ANKRD26
c.-140C>G
p.?
This variant

The ANKRD26 c.-140C>G (NP_055730.2:p.?) variant has not been observed in somatic cancers in COSMIC and has been reported in ClinVar as Benign.

Transcript
NM_014915.2
HGVS · transcript:coding
NM_014915.2:c.-140C>G
GRCh38
chr10:27100466 G>C
GRCh37
chr10:27389395 G>C
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback.
Classification rationale
BA1BS1 Benign
ANKRD26 c.-140C>G

The ANKRD26 c.-140C>G (NP_055730.2:p.?) variant has not been observed in somatic cancers in COSMIC and has been reported in ClinVar as Benign.1 This variant is common in population databases, with allele frequencies of 0.0640054 (6.40054%) in gnomAD v2.1 and 0.0478907 (4.78907%) in gnomAD v4.1, which are well above benign thresholds.2 In silico splice prediction does not support a splice-altering effect, with a SpliceAI maximum delta score of 0.07.3

BA1 + BS1 Benign
LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.
Gene diagram · NM_014915.2 · variants mapped to exon structure
ANKRD26 NM_014915.2
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 18 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 2
Strength Supporting Moderate Strong Very strong
BA1 stand-alone Benign
This variant is far above the benign stand-alone population threshold. The allele frequency is 0.0640054 (6.40054%) in gnomAD v2.1 and 0.0478907 (4.78907%) in gnomAD v4.1, both above the BA1 threshold of 0.01 (1%), supporting BA1.
gnomAD v2.1 total AF 0.0640054African/African American AF 0.085304269 homozygotes.
BS1 strong Benign
The population frequency is also well above the strong benign threshold. The allele frequency is 0.0640054 in gnomAD v2.1 and 0.0478907 in gnomAD v4.1, both above the BS1 threshold of 0.003 (0.3%), so BS1 is met.
gnomAD v2.1 total AF 0.0640054grpmax FAF 0.0802218.gnomAD v4.1 total AF 0.0478907
Assessed · not applied · 4 not met · 14 not assessed
Pathogenic
PS2 No confirmed de novo data with verified maternity and paternity were identified, so PS2 cannot be assessed.
PS3 No validated functional studies demonstrating a damaging effect of this specific variant were identified from the available evidence, so PS3 was not assessed.
PS4 This variant has not been observed in COSMIC and is listed in ClinVar as Benign; no case-control or enrichment data showing increased prevalence in affected individuals were identified, so PS4 is not met.
PM1 No established mutational hotspot or well-characterized critical functional region for applying PM1 to this specific 5'UTR position was identified in the available evidence.
PM2 This variant is common in population databases rather than absent or rare.
PM3 No data were identified showing this variant in trans with a pathogenic variant in a recessive disorder, so PM3 was not assessed.
PM6 No assumed de novo occurrence data were identified, so PM6 was not assessed.
PP1 No segregation data were identified, so PP1 was not assessed.
PP3 Available computational evidence does not support a damaging effect on splicing.
PP4 No phenotype-specific evidence was identified showing a clinical presentation highly specific for a disorder caused by this variant, so PP4 was not assessed.
PP5 Although ClinVar lists this variant as Benign, PP5 was not used because this criterion concerns pathogenic assertions from a reputable source and independent evidence is available.
Benign
BS2 Population databases show many homozygotes, but no direct evidence was identified confirming unaffected status in a setting appropriate for BS2, so this criterion was not assessed.
BS3 No well-established functional studies demonstrating no damaging effect of this specific variant were formally curated in the available evidence for BS3 application.
BS4 No segregation studies showing lack of cosegregation with disease were identified, so BS4 was not assessed.
BP2 No phase data were identified showing this variant in trans with a pathogenic variant for a dominant disorder or in cis with a pathogenic variant in any relevant setting, so BP2 was not assessed.
BP4 SpliceAI predicts no significant splice impact, with a maximum delta score of 0.07, but this isolated splice prediction does not fully establish a benign effect for a 5'UTR regulatory variant.
BP5 No alternate molecular explanation for the reported phenotype was identified from the available evidence, so BP5 was not assessed.
BP6 ClinVar reports this variant as Benign, but BP6 was not used because the submission is not from an expert panel and strong independent benign population evidence is already available.
N/A · 8 PVS1 · PS1 · PM4 · PM5 · PP2 · BP1 · BP3 · BP7
Research & evidence
Population frequency · supports benign
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= 0.0478907; MAF= 4.78907%, 62124/1297204 alleles, homozygotes = 1684) and has highest observed frequency in the African/African American population (AF= 0.0837021; MAF= 8.37021%, 5637/67346 alleles, homozygotes = 245); grpmax FAF= 0.0818764.
v2.1
This variant is present in gnomAD v2.1 (AF= 0.0640054; MAF= 6.40054%, 2009/31388 alleles, homozygotes = 69) and has highest observed frequency in the African/African American population (AF= 0.0853042; MAF= 8.53042%, 743/8710 alleles, homozygotes = 34); grpmax FAF= 0.0802218.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
4.8% · 62124 / 1,297,204
1684 hom · FAF 8.2%
African/African American
5637 / 67,346
8.4%
245 hom
Ashkenazi Jewish
1595 / 22,702
7%
42 hom
European (Finnish)
2280 / 42,134
5.4%
53 hom
European (non-Finnish)
46842 / 960,288
4.9%
1212 hom
Remaining individuals
2409 / 51,146
4.7%
56 hom
Middle Eastern
162 / 3,700
4.4%
6 hom
South Asian
2093 / 69,972
3%
53 hom
Admixed American
1007 / 38,008
2.6%
15 hom
Amish
20 / 908
2.2%
1 hom
East Asian
79 / 41,000
0.19%
1 hom
gnomAD v2.1
6.4% · 2009 / 31,388
69 hom · FAF 8%
African/African American
743 / 8,710
8.5%
34 hom
Ashkenazi Jewish
22 / 288
7.6%
Remaining individuals
71 / 1,088
6.5%
2 hom
European (non-Finnish)
957 / 15,420
6.2%
26 hom
European (Finnish)
191 / 3,474
5.5%
7 hom
Admixed American
21 / 848
2.5%
East Asian
4 / 1,560
0.26%
+ 1 not observed (South Asian)
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar as Benign (8 clinical laboratories).
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.07).
Functional No data
No calibrated functional assay or RNA evidence was identified for this variant.
OncoKB ↗
COSMIC screenshot
COSMIC
Somatic evidence
COSMIC
This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant cancer hotspot.
COSMIC ↗
Sources & reference links
6Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
SpliceAI
OncoKB
COSMIC