rs13061797

Positions:

• chr3-161827209-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;