rs332188

chr10-28625093-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 0.561 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.675

Gnomad4 SAS AF: 0.668

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.568

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs332188; hg19: chr10-28914022;