rs10982360

Variant names:

• chr9-114655662-C-T
• rs10982360

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 0.337 in 151,908 control chromosomes in the GnomAD database, including 9,347 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 0.34 (9347 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 4 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 (AFR) allele frequency at 95% confidence interval = 0.462 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: 0.337 AC: 51085 AN: 151790 Hom.: 9312 Cov.: 31

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.337 AC: 51167 AN: 151908 Hom.: 9347 Cov.: 31 AF XY: 0.339 AC XY: 25133 AN XY: 74246

African (AFR) AF: 0.467 AC: 19353 AN: 41410

American (AMR) AF: 0.343 AC: 5228 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1342 AN: 3472

East Asian (EAS) AF: 0.319 AC: 1642 AN: 5146

South Asian (SAS) AF: 0.444 AC: 2136 AN: 4806

European-Finnish (FIN) AF: 0.251 AC: 2648 AN: 10554

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17703 AN: 67946

Other (OTH) AF: 0.332 AC: 700 AN: 2108

Alfa AF: 0.297 Hom.: 5690

Bravo AF: 0.350

Asia WGS AF: 0.428 AC: 1488 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	0.63
DANN	Benign	0.59
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10982360; hg19: chr9-117417942;