rs903051

Variant names:

• chr3-148664618-G-A
• rs903051

Your query was ambiguous. Multiple possible variants found:

• chr3-148664618-G-A
• chr3-148664618-G-C

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 0.563 in 151,862 control chromosomes in the GnomAD database, including 25,336 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 0.56 (25336 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.79 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: 0.563 AC: 85403 AN: 151744 Hom.: 25315 Cov.: 31

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.563 AC: 85468 AN: 151862 Hom.: 25336 Cov.: 31 AF XY: 0.568 AC XY: 42179 AN XY: 74232

Gnomad4 AFR AF: 0.373

Gnomad4 AMR AF: 0.695

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.810

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.675

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.559

Alfa AF: 0.590 Hom.: 4211

Bravo AF: 0.561

Asia WGS AF: 0.646 AC: 2247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.6
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs903051; hg19: chr3-148382405;