rs10982360

chr9-114655662-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 0.337 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.332

Alfa AF: 0.299 Hom.: 4840

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10982360; hg19: chr9-117417942;