rs3916958

Variant names:

• chr13-105130610-G-A
• rs3916958

Your query was ambiguous. Multiple possible variants found:

• chr13-105130610-G-A
• chr13-105130610-G-C
• chr13-105130610-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;