rs827382

Variant names:

• chr10-8677306-C-T
• rs827382

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 0.736 in 151,992 control chromosomes in the GnomAD database, including 41,456 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 0.74 (41456 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.32
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.812 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: 0.737 AC: 111856 AN: 151874 Hom.: 41424 Cov.: 31

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.763

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.736 AC: 111942 AN: 151992 Hom.: 41456 Cov.: 31 AF XY: 0.738 AC XY: 54793 AN XY: 74268

African (AFR) AF: 0.700 AC: 29026 AN: 41456

American (AMR) AF: 0.824 AC: 12574 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.777 AC: 2693 AN: 3468

East Asian (EAS) AF: 0.763 AC: 3929 AN: 5148

South Asian (SAS) AF: 0.747 AC: 3601 AN: 4818

European-Finnish (FIN) AF: 0.746 AC: 7887 AN: 10570

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.734 AC: 49868 AN: 67962

Other (OTH) AF: 0.752 AC: 1583 AN: 2106

Alfa AF: 0.744 Hom.: 23358

Bravo AF: 0.743

Asia WGS AF: 0.735 AC: 2556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.64
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs827382; hg19: chr10-8719269; COSMIC: COSV69614774;