rs827382

chr10-8677306-C-T

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 0.736 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.700

Gnomad4 AMR AF: 0.824

Gnomad4 ASJ AF: 0.777

Gnomad4 EAS AF: 0.763

Gnomad4 SAS AF: 0.747

Gnomad4 FIN AF: 0.746

Gnomad4 NFE AF: 0.734

Gnomad4 OTH AF: 0.752

Alfa AF: 0.746 Hom.: 13006

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

Splicing

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

Publications

LitVar

Other links and lift over

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