3-161796007-T-C

Variant names:

• chr3-161796007-T-C
• rs11918801

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.444 in 151,926 control chromosomes in the GnomAD database, including 15,659 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 0.44 (15659 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.825 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: 0.444 AC: 67398 AN: 151808 Hom.: 15641 Cov.: 32

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.444 AC: 67444 AN: 151926 Hom.: 15659 Cov.: 32 AF XY: 0.450 AC XY: 33424 AN XY: 74254

African (AFR) AF: 0.367 AC: 15201 AN: 41434

American (AMR) AF: 0.496 AC: 7566 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1572 AN: 3468

East Asian (EAS) AF: 0.846 AC: 4373 AN: 5172

South Asian (SAS) AF: 0.409 AC: 1965 AN: 4808

European-Finnish (FIN) AF: 0.523 AC: 5511 AN: 10544

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 30015 AN: 67936

Other (OTH) AF: 0.434 AC: 915 AN: 2108

Alfa AF: 0.435 Hom.: 7546

Bravo AF: 0.447

Asia WGS AF: 0.632 AC: 2194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.9
DANN	Benign	0.48
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs11918801; hg19: chr3-161513795;