chr3-152770251-T-C

Variant names:

• chr3-152770251-T-C
• rs9875837

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 0.581 in 151,852 control chromosomes in the GnomAD database, including 26,976 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 0.58 (26976 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.713 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: 0.582 AC: 88244 AN: 151734 Hom.: 26962 Cov.: 31

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.581 AC: 88287 AN: 151852 Hom.: 26976 Cov.: 31 AF XY: 0.584 AC XY: 43327 AN XY: 74242

African (AFR) AF: 0.372 AC: 15400 AN: 41428

American (AMR) AF: 0.684 AC: 10439 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2235 AN: 3466

East Asian (EAS) AF: 0.732 AC: 3773 AN: 5154

South Asian (SAS) AF: 0.725 AC: 3489 AN: 4812

European-Finnish (FIN) AF: 0.617 AC: 6494 AN: 10524

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.655 AC: 44463 AN: 67886

Other (OTH) AF: 0.593 AC: 1250 AN: 2108

Alfa AF: 0.642 Hom.: 16155

Bravo AF: 0.573

Asia WGS AF: 0.717 AC: 2490 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.6
DANN	Benign	0.57
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs9875837; hg19: chr3-152488040;