rs9851460

Positions:

• chr3-155184467-A-G

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 0.683 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.660

Gnomad4 AMR AF: 0.688

Gnomad4 ASJ AF: 0.665

Gnomad4 EAS AF: 0.710

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.655

Gnomad4 NFE AF: 0.700

Gnomad4 OTH AF: 0.690

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9851460; hg19: chr3-154902256;