rs13061797

Variant names:

• chr3-161827209-T-C
• rs13061797

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 0.134 in 151,642 control chromosomes in the GnomAD database, including 1,513 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 0.13 (1513 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.556

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 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: 0.134 AC: 20288 AN: 151524 Hom.: 1512 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.0117

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0962

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.134 AC: 20296 AN: 151642 Hom.: 1513 Cov.: 32 AF XY: 0.130 AC XY: 9658 AN XY: 74106

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.0115

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.0962

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.145

Alfa AF: 0.145 Hom.: 1104

Bravo AF: 0.136

Asia WGS AF: 0.0710 AC: 249 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.1
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13061797; hg19: chr3-161544997;