rs10962656

chr9-16877790-G-A

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 0.102 in 152,172 control chromosomes in the GnomAD database, including 1,030 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 0.10 (1030 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588

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 = 0.152 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: 0.103 AC: 15589 AN: 152054 Hom.: 1029 Cov.: 32

Gnomad AFR AF: 0.0249

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.0748

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0565

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.0938

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

GnomAD4 genome AF: 0.102 AC: 15587 AN: 152172 Hom.: 1030 Cov.: 32 AF XY: 0.101 AC XY: 7482 AN XY: 74384

Gnomad4 AFR AF: 0.0248

Gnomad4 AMR AF: 0.0746

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0574

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.0923

Alfa AF: 0.136 Hom.: 668

Bravo AF: 0.0924

Asia WGS AF: 0.0290 AC: 102 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	1.9
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10962656; hg19: chr9-16877788;