3-162979680-A-T

Variant names:

• chr3-162979680-A-T
• rs10513597

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0999 in 151,798 control chromosomes in the GnomAD database, including 794 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 0.10 (794 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.35
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15166 AN: 151680 Hom.: 794 Cov.: 31

Gnomad AFR AF: 0.0988

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0929

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0803

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.0999 AC: 15159 AN: 151798 Hom.: 794 Cov.: 31 AF XY: 0.0981 AC XY: 7280 AN XY: 74180

African (AFR) AF: 0.0985 AC: 4082 AN: 41434

American (AMR) AF: 0.101 AC: 1532 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.0929 AC: 322 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.0795 AC: 382 AN: 4804

European-Finnish (FIN) AF: 0.116 AC: 1227 AN: 10570

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7278 AN: 67858

Other (OTH) AF: 0.120 AC: 253 AN: 2100

Alfa AF: 0.0943 Hom.: 86

Bravo AF: 0.0981

Asia WGS AF: 0.0460 AC: 159 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	18
DANN	Benign	0.65
PhyloP100		2.4

Splicing

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

Other links and lift over

dbSNP: rs10513597; hg19: chr3-162697468;