3-162915819-G-A

Variant names:

• chr3-162915819-G-A
• rs13094783

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 0.326 in 150,876 control chromosomes in the GnomAD database, including 8,168 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 0.33 (8168 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.509
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49155 AN: 150756 Hom.: 8160 Cov.: 31

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.326 AC: 49185 AN: 150876 Hom.: 8168 Cov.: 31 AF XY: 0.334 AC XY: 24595 AN XY: 73734

African (AFR) AF: 0.316 AC: 13050 AN: 41310

American (AMR) AF: 0.313 AC: 4720 AN: 15068

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1051 AN: 3444

East Asian (EAS) AF: 0.110 AC: 567 AN: 5134

South Asian (SAS) AF: 0.424 AC: 2035 AN: 4802

European-Finnish (FIN) AF: 0.456 AC: 4796 AN: 10524

Middle Eastern (MID) AF: 0.226 AC: 66 AN: 292

European-Non Finnish (NFE) AF: 0.325 AC: 21860 AN: 67294

Other (OTH) AF: 0.282 AC: 592 AN: 2098

Alfa AF: 0.327 Hom.: 1599

Bravo AF: 0.314

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.64
DANN	Benign	0.14
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs13094783; hg19: chr3-162633607;