rs962993

Variant names:

• chr10-9011169-C-T
• rs962993

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 0.334 in 151,752 control chromosomes in the GnomAD database, including 9,189 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 0.33 (9189 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.408 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: 0.334 AC: 50711 AN: 151632 Hom.: 9190 Cov.: 31

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.334 AC: 50714 AN: 151752 Hom.: 9189 Cov.: 31 AF XY: 0.326 AC XY: 24154 AN XY: 74144

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.374

Alfa AF: 0.382 Hom.: 4878

Bravo AF: 0.331

Asia WGS AF: 0.233 AC: 812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs962993; hg19: chr10-9053132;