rs827640

Positions:

• chr10-8946048-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 0.387 in 151,572 control chromosomes in the GnomAD database, including 11,917 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 0.39 (11917 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.651 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: 0.387 AC: 58654 AN: 151454 Hom.: 11895 Cov.: 31

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.387 AC: 58717 AN: 151572 Hom.: 11917 Cov.: 31 AF XY: 0.387 AC XY: 28642 AN XY: 74034

Gnomad4 AFR AF: 0.401

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.669

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.436

Alfa AF: 0.359 Hom.: 2316

Bravo AF: 0.409

Asia WGS AF: 0.562 AC: 1948 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs827640; hg19: chr10-8988011;