3-10161506-A-T

Variant names:

• chr3-10161506-A-T
• rs464396

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 0.784 in 151,920 control chromosomes in the GnomAD database, including 47,595 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 0.78 (47595 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.771
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.859 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: 0.784 AC: 119002 AN: 151802 Hom.: 47571 Cov.: 31

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.911

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.802

Gnomad FIN AF: 0.876

Gnomad MID AF: 0.793

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.795

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

GnomAD4 genome AF: 0.784 AC: 119067 AN: 151920 Hom.: 47595 Cov.: 31 AF XY: 0.788 AC XY: 58511 AN XY: 74252

African (AFR) AF: 0.613 AC: 25404 AN: 41428

American (AMR) AF: 0.821 AC: 12533 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.911 AC: 3159 AN: 3466

East Asian (EAS) AF: 0.880 AC: 4539 AN: 5158

South Asian (SAS) AF: 0.801 AC: 3868 AN: 4826

European-Finnish (FIN) AF: 0.876 AC: 9250 AN: 10562

Middle Eastern (MID) AF: 0.791 AC: 231 AN: 292

European-Non Finnish (NFE) AF: 0.849 AC: 57631 AN: 67902

Other (OTH) AF: 0.788 AC: 1665 AN: 2114

Alfa AF: 0.786 Hom.: 2914

Bravo AF: 0.774

Asia WGS AF: 0.813 AC: 2830 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.43
DANN	Benign	0.71
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs464396; hg19: chr3-10203190;