rs332188

Variant names:

• chr10-28625093-G-C
• rs332188

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 0.561 in 152,018 control chromosomes in the GnomAD database, including 24,343 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 (24343 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.656 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: 0.561 AC: 85192 AN: 151900 Hom.: 24299 Cov.: 32

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.561 AC: 85294 AN: 152018 Hom.: 24343 Cov.: 32 AF XY: 0.563 AC XY: 41830 AN XY: 74298

African (AFR) AF: 0.619 AC: 25693 AN: 41478

American (AMR) AF: 0.606 AC: 9247 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1989 AN: 3468

East Asian (EAS) AF: 0.675 AC: 3481 AN: 5158

South Asian (SAS) AF: 0.668 AC: 3220 AN: 4822

European-Finnish (FIN) AF: 0.433 AC: 4568 AN: 10554

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35326 AN: 67956

Other (OTH) AF: 0.568 AC: 1200 AN: 2112

Alfa AF: 0.543 Hom.: 2791

Bravo AF: 0.573

Asia WGS AF: 0.676 AC: 2352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.14
DANN	Benign	0.59
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs332188; hg19: chr10-28914022;