rs907931

chr3-129949941-G-Achr3-129949941-G-Cchr3-129949941-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.741 in 152,100 control chromosomes in the GnomAD database, including 42,933 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.74 (42933 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.889

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.741 AC: 112592 AN: 151982 Hom.: 42899 Cov.: 31

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.819

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.831

Gnomad OTH AF: 0.764

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.741 AC: 112680 AN: 152100 Hom.: 42933 Cov.: 31 AF XY: 0.739 AC XY: 54908 AN XY: 74344

Gnomad4 AFR AF: 0.554

Gnomad4 AMR AF: 0.820

Gnomad4 ASJ AF: 0.803

Gnomad4 EAS AF: 0.715

Gnomad4 SAS AF: 0.818

Gnomad4 FIN AF: 0.723

Gnomad4 NFE AF: 0.831

Gnomad4 OTH AF: 0.765

Alfa AF: 0.757 Hom.: 4211

Bravo AF: 0.740

Asia WGS AF: 0.748 AC: 2602 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.23
Dann	Benign	0.49

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs907931; hg19: chr3-129668784;