chr3-10161506-A-T

Variant names:

• chr3-10161506-A-T
• rs464396

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 0.784 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.784 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

Gnomad4 AFR AF: 0.613

Gnomad4 AMR AF: 0.821

Gnomad4 ASJ AF: 0.911

Gnomad4 EAS AF: 0.880

Gnomad4 SAS AF: 0.801

Gnomad4 FIN AF: 0.876

Gnomad4 NFE AF: 0.849

Gnomad4 OTH AF: 0.788

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs464396; hg19: chr3-10203190;