rs850303

Variant names:

• chr3-187302412-C-A
• rs850303

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 0.174 in 152,018 control chromosomes in the GnomAD database, including 2,409 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 0.17 (2409 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400
• Publications: 6 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 (SAS) allele frequency at 95% confidence interval = 0.191 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: 0.174 AC: 26457 AN: 151898 Hom.: 2402 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.174 AC: 26479 AN: 152018 Hom.: 2409 Cov.: 32 AF XY: 0.171 AC XY: 12715 AN XY: 74322

African (AFR) AF: 0.152 AC: 6318 AN: 41448

American (AMR) AF: 0.166 AC: 2531 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 818 AN: 3464

East Asian (EAS) AF: 0.193 AC: 1000 AN: 5174

South Asian (SAS) AF: 0.201 AC: 970 AN: 4816

European-Finnish (FIN) AF: 0.148 AC: 1567 AN: 10558

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12712 AN: 67968

Other (OTH) AF: 0.171 AC: 361 AN: 2108

Alfa AF: 0.184 Hom.: 4223

Bravo AF: 0.173

Asia WGS AF: 0.216 AC: 755 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	0.74
DANN	Benign	0.44
PhyloP100		-0.040

Splicing

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

Other links and lift over

dbSNP: rs850303; hg19: chr3-187020200;