rs9851460

Variant names:

• chr3-155184467-A-G
• rs9851460

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 0.683 in 152,052 control chromosomes in the GnomAD database, including 35,520 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 0.68 (35520 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.695 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: 0.683 AC: 103751 AN: 151934 Hom.: 35502 Cov.: 32

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.683 AC: 103826 AN: 152052 Hom.: 35520 Cov.: 32 AF XY: 0.680 AC XY: 50546 AN XY: 74314

African (AFR) AF: 0.660 AC: 27342 AN: 41458

American (AMR) AF: 0.688 AC: 10513 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.665 AC: 2308 AN: 3470

East Asian (EAS) AF: 0.710 AC: 3664 AN: 5164

South Asian (SAS) AF: 0.628 AC: 3030 AN: 4826

European-Finnish (FIN) AF: 0.655 AC: 6927 AN: 10572

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.700 AC: 47585 AN: 67976

Other (OTH) AF: 0.690 AC: 1458 AN: 2112

Alfa AF: 0.696 Hom.: 9025

Bravo AF: 0.688

Asia WGS AF: 0.671 AC: 2332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.93
DANN	Benign	0.26
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs9851460; hg19: chr3-154902256;