rs3916958

chr13-105130610-G-Achr13-105130610-G-Cchr13-105130610-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 0.55 in 151,708 control chromosomes in the GnomAD database, including 23,314 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 0.55 (23314 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.677

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 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: 0.550 AC: 83408 AN: 151592 Hom.: 23297 Cov.: 31

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.550 AC: 83475 AN: 151708 Hom.: 23314 Cov.: 31 AF XY: 0.546 AC XY: 40469 AN XY: 74150

Gnomad4 AFR AF: 0.623

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.525

Gnomad4 FIN AF: 0.559

Gnomad4 NFE AF: 0.541

Gnomad4 OTH AF: 0.547

Alfa AF: 0.530 Hom.: 26190

Bravo AF: 0.540

Asia WGS AF: 0.508 AC: 1761 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.89
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3916958; hg19: chr13-105782961;