rs950753

Variant names:

• chr3-30067901-C-T
• rs950753

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 0.261 in 151,952 control chromosomes in the GnomAD database, including 5,326 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 0.26 (5326 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.338 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: 0.261 AC: 39554 AN: 151834 Hom.: 5315 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.261 AC: 39589 AN: 151952 Hom.: 5326 Cov.: 32 AF XY: 0.260 AC XY: 19268 AN XY: 74242

African (AFR) AF: 0.247 AC: 10231 AN: 41440

American (AMR) AF: 0.265 AC: 4047 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1029 AN: 3470

East Asian (EAS) AF: 0.351 AC: 1802 AN: 5130

South Asian (SAS) AF: 0.162 AC: 778 AN: 4806

European-Finnish (FIN) AF: 0.274 AC: 2894 AN: 10560

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.263 AC: 17878 AN: 67972

Other (OTH) AF: 0.276 AC: 582 AN: 2110

Alfa AF: 0.252 Hom.: 628

Bravo AF: 0.265

Asia WGS AF: 0.288 AC: 1000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.77
DANN	Benign	0.27
PhyloP100		0.097

Splicing

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

Other links and lift over

dbSNP: rs950753; hg19: chr3-30109392;