rs903051

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;