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NM_024426.4:c.1107A>G
p.Arg369= · WT1
ACMG/AMP
0%
complete
Final classification
Benign
BA1BS1BP4BP7
WT1
c.1107A>G
p.Arg369=
This variant

The WT1 c.1107A>G (p.Arg369=) variant has been reported in ClinVar as benign.

Transcript
NM_024426.4
HGVS · transcript:coding
NM_024426.4:c.1107A>G
GRCh38
chr11:32396399 T>C
GRCh37
chr11:32417945 T>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
BA1BS1BP4BP7 Benign
WT1 c.1107A>G

The WT1 c.1107A>G (p.Arg369=) variant has been reported in ClinVar as benign.1 This variant is common in population databases, with an allele frequency of 0.235708 in gnomAD v2.1 and 0.180386 in gnomAD v4.1, which is far above benign population thresholds.2 In silico evidence supports a benign interpretation because this synonymous change does not alter the encoded amino acid and SpliceAI predicts no significant splice impact with a maximum delta score of 0.01.3

BA1 + BS1 + BP4 + BP7 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_024426.4 · variants mapped to exon structure
WT1 NM_024426.4
Fetching transcript structure from UCSC…
Applied criteria · 4 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 · 4
Strength Supporting Moderate Strong Very strong
BA1 stand-alone Benign
Population frequency is well above the benign stand-alone threshold of 0.01. This variant is present in gnomAD v2.1 at AF 0.235708 and in gnomAD v4.1 at AF 0.180386, with East Asian frequencies of 0.697872 and 0.671155, respectively.
gnomAD v2.1 AF 0.235708East Asian AF 0.697872gnomAD v4.1 AF 0.180386
BS1 strong Benign
Population frequency is above the strong benign threshold of 0.003. This variant is present in gnomAD v2.1 at AF 0.235708 and in gnomAD v4.1 at AF 0.180386, both greatly exceeding that threshold.
gnomAD v2.1 AF 0.235708gnomAD v4.1 AF 0.180386
BP4 supporting Benign
Available computational evidence supports no impact on the gene product or splicing. The variant is synonymous, p.(Arg369=), and SpliceAI predicts no significant splice impact with a maximum delta score of 0.01.
synonymous protein prediction p.(Arg369=)SpliceAI max delta score 0.01
BP7 supporting Benign
This is a synonymous variant, WT1 c.1107A>G (p.Arg369=), and SpliceAI predicts no significant splice impact with a maximum delta score of 0.01, supporting no effect on RNA splicing.
synonymous protein prediction p.(Arg369=)SpliceAI max delta score 0.01
Assessed · not applied · 5 not met · 13 not assessed
Pathogenic
PVS1 This variant is a synonymous change, WT1 c.1107A>G (p.Arg369=), and does not fall within the generic PVS1 null-variant categories for nonsense, frameshift, or canonical +/-1 or 2 splice-site variants.
PS2 No confirmed de novo data with established maternity and paternity were identified for this variant.
PS3 No well-established functional studies demonstrating a damaging effect of this specific variant were identified.
PS4 Available evidence does not show that this variant is enriched in individuals with WT1-related germline disease compared with controls.
PM1 This variant does not lie in a statistically significant hotspot, so available evidence does not support location in a critical mutational hot spot or well-established functional domain without benign variation.
PM2 This variant is not absent from population databases.
PM3 No data were identified showing this variant in trans with a pathogenic variant in a recessive disorder.
PM6 No assumed de novo occurrence data were identified for this variant.
PP1 No segregation data were identified showing this variant tracking with disease in affected family members.
PP3 Available computational evidence does not support a deleterious effect.
PP4 No individual-level phenotype data were identified to show a WT1-related clinical presentation that is highly specific for disease caused by this variant.
PP5 An external clinical database classification was identified, but this criterion was not used as stand-alone evidence for pathogenicity.
Benign
BS2 The variant is observed many times in population databases, including numerous homozygotes, but phenotype-confirmed healthy adult observations were not identified for formal BS2 application.
BS3 No well-established functional studies showing a benign effect of this specific variant were identified.
BS4 No family data were identified showing lack of segregation with disease.
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.
BP5 No evidence was identified for an alternate molecular explanation that would account for the observed phenotype independently of this variant.
BP6 An external clinical database classification was identified, but this criterion was not used as stand-alone evidence for benignity.
N/A · 6 PS1 · PM4 · PM5 · PP2 · BP1 · BP3
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= 0.180386; MAF= 18.03862%, 291078/1613638 alleles, homozygotes = 35597) and has highest observed frequency in the East Asian population (AF= 0.671155; MAF= 67.11547%, 30108/44860 alleles, homozygotes = 10092); grpmax FAF= 0.664805.
v2.1
This variant is present in gnomAD v2.1 (AF= 0.235708; MAF= 23.57076%, 66569/282422 alleles, homozygotes = 11532) and has highest observed frequency in the East Asian population (AF= 0.697872; MAF= 69.78717%, 13903/19922 alleles, homozygotes = 4884); grpmax FAF= 0.685973.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
18% · 291078 / 1,613,638
35597 hom · FAF 66%
East Asian
30108 / 44,860
67%
10092 hom
South Asian
32191 / 91,058
35%
5879 hom
Admixed American
20521 / 59,984
34%
3749 hom
Remaining individuals
12655 / 62,492
20%
1606 hom
Amish
179 / 910
20%
23 hom
Middle Eastern
1124 / 5,992
19%
117 hom
Ashkenazi Jewish
5273 / 29,608
18%
452 hom
European (Finnish)
10979 / 63,800
17%
959 hom
European (non-Finnish)
169781 / 1,179,968
14%
12283 hom
African/African American
8267 / 74,966
11%
437 hom
gnomAD v2.1
24% · 66569 / 282,422
11532 hom · FAF 69%
East Asian
13903 / 19,922
70%
4884 hom
Admixed American
13014 / 35,402
37%
2537 hom
South Asian
10896 / 30,608
36%
1975 hom
Remaining individuals
1419 / 7,212
20%
140 hom
Ashkenazi Jewish
1832 / 10,368
18%
156 hom
European (Finnish)
4363 / 24,938
17%
363 hom
European (non-Finnish)
18363 / 129,014
14%
1329 hom
African/African American
2779 / 24,958
11%
148 hom
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar as Benign (20 clinical laboratories) and as benign (1 clinical laboratory).
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01).
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB oncogenicity for this specific variant: Unknown Oncogenic Effect (variant has not been individually curated).
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; COSV60066333, n = 111 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