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NM_000465.4:c.62G>T
p.Arg21Leu · BARD1
ACMG/AMP
0%
complete
Final classification
VUS
PM2BP4
BARD1
c.62G>T
p.Arg21Leu
This variant

The BARD1 c.62G>T (p.Arg21Leu) variant has not been identified in a statistically significant cancer hotspot and has been reported in ClinVar as a variant of uncertain significance by a single submitter.

Transcript
NM_000465.4
HGVS · transcript:coding
NM_000465.4:c.62G>T
GRCh38
chr2:214809508 C>A
GRCh37
chr2:215674232 C>A
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting, BP4 supporting; combination = 1 supporting + 1 supporting benign, which maps to VUS because the evidence is conflicting.
Classification rationale
PM2 BP4 VUS
BARD1 c.62G>T

The BARD1 c.62G>T (p.Arg21Leu) variant has not been identified in a statistically significant cancer hotspot and has been reported in ClinVar as a variant of uncertain significance by a single submitter.1 This variant is absent from gnomAD v2.1 and has 0/1,601,354 alleles in gnomAD v4.1 (AF 0.0%), which is below the 0.1% threshold used for PM2 and supports rarity in population databases.2 Available computational evidence does not support a damaging effect, with a REVEL score of 0.16 and a BayesDel score of -0.392235, supporting benign computational evidence rather than pathogenic computational evidence.

PM2 + BP4 VUS
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_000465.4 · variants mapped to exon structure
BARD1 NM_000465.4
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 21 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
PM2 supporting review Pathogenic
This variant is absent from gnomAD v2.1 and has 0/1,601,354 alleles in gnomAD v4.1 (AF 0.0%), which is below the 0.1% rarity threshold used for PM2 in this framework. This supports that the variant is rare in population databases.
gnomAD v2.1: absentgnomAD v4.1: 0/1601354 allelesAF 0.0%
BP4 supporting review Benign
Available computational evidence favors a benign effect for this missense change. REVEL is 0.16 and BayesDel is -0.392235, which do not support a damaging protein effect.
REVEL 0.16BayesDel -0.392235
Assessed · not applied · 6 not met · 15 not assessed
Pathogenic
PS1 No evidence was identified showing that another nucleotide change causing the same amino acid substitution, p.(Arg21Leu), has already been established as pathogenic or likely pathogenic.
PS2 No confirmed de novo observation with verified maternity and paternity was identified.
PS3 No well-established functional study showing a damaging effect of this specific variant was identified.
PS4 No case-control enrichment or multiple independent affected observations were identified to show that this variant is significantly increased in affected individuals over controls.
PM1 This variant has not been identified in a statistically significant hotspot, and available evidence does not show that codon 21 lies in a well-established critical region without benign variation.
PM5 No evidence was identified showing that a different missense change at the same amino acid residue has already been established as pathogenic or likely pathogenic.
PM6 No assumed de novo observation without confirmed parentage was identified.
PP1 No segregation data were identified to show that this variant tracks with disease in affected family members.
PP2 Available evidence does not establish that pathogenic missense variation is a common disease mechanism in BARD1 or that this gene has a low rate of benign missense variation sufficient for PP2.
PP3 Available computational evidence does not support a deleterious effect.
PP4 No phenotype or family history data were identified showing a highly specific clinical presentation attributable to a single genetic cause for this variant assessment.
PP5 ClinVar reports this variant as uncertain significance rather than pathogenic or likely pathogenic, so external classification evidence does not support PP5.
Benign
BA1 Population frequency does not meet the standalone benign threshold.
BS1 Population frequency does not support a benign interpretation.
BS2 No evidence was identified showing this variant in healthy adult individuals in a manner sufficient to support a benign classification.
BS3 No well-established functional study showing a normal or benign effect for this specific variant was identified.
BS4 No segregation data were identified showing lack of segregation with disease.
BP1 Available evidence does not establish that missense variants in BARD1 are generally less likely to be pathogenic than truncating variants to a degree sufficient for BP1.
BP2 No phase data were identified showing this variant in trans with a pathogenic variant for a fully penetrant dominant disorder, or in cis with a pathogenic variant in a way that would support BP2.
BP5 No alternate molecular explanation was identified for the phenotype that would support BP5.
BP6 ClinVar does not report this variant as benign or likely benign, so external classification evidence does not support BP6.
N/A · 5 PVS1 · PM3 · PM4 · BP3 · 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; MAF= 0.00000%, 0/1601354 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/74788 alleles, homozygotes = 0).
v2.1
Absent from gnomAD v2.1.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent · 0 / 1,601,354
0 hom
Not observed in any ancestry group.
+ 10 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American, European (non-Finnish))
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar as Uncertain significance (1 clinical laboratory).
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.16. BayesDel score = -0.392235.
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB has not reviewed this specific variant; no variant-level oncogenicity or biological effect is available. Gene-level context: BARD1, a tumor suppressor involved in the DNA damage response, is altered by mutation in breast and ovarian cancers.
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 previously been reported in somatic cancers (COSMIC; COSV53613702, n = 1 times).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
7Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
SpliceAI
OncoKB
COSMIC
Cancer hotspots