10-73934174-T-C

Variant names:

• chr10-73934174-T-C
• rs2633322

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 0.668 in 151,998 control chromosomes in the GnomAD database, including 34,635 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 0.67 (34635 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.294
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.74 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: 0.668 AC: 101505 AN: 151880 Hom.: 34636 Cov.: 31

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.895

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.668 AC: 101533 AN: 151998 Hom.: 34635 Cov.: 31 AF XY: 0.659 AC XY: 48914 AN XY: 74256

African (AFR) AF: 0.603 AC: 24974 AN: 41448

American (AMR) AF: 0.574 AC: 8762 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.895 AC: 3109 AN: 3472

East Asian (EAS) AF: 0.496 AC: 2559 AN: 5160

South Asian (SAS) AF: 0.572 AC: 2746 AN: 4798

European-Finnish (FIN) AF: 0.591 AC: 6244 AN: 10566

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.746 AC: 50686 AN: 67966

Other (OTH) AF: 0.736 AC: 1552 AN: 2110

Alfa AF: 0.734 Hom.: 62171

Bravo AF: 0.666

Asia WGS AF: 0.505 AC: 1761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.63
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs2633322; hg19: chr10-75693932;