rs10962656

Variant names:

• chr9-16877790-G-A
• rs10962656

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 0.102 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0248 AC: 1031 AN: 41536

American (AMR) AF: 0.0746 AC: 1140 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 521 AN: 3468

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5160

South Asian (SAS) AF: 0.0574 AC: 277 AN: 4824

European-Finnish (FIN) AF: 0.163 AC: 1728 AN: 10574

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10510 AN: 68002

Other (OTH) AF: 0.0923 AC: 195 AN: 2112

Alfa AF: 0.137 Hom.: 758

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
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs10962656; hg19: chr9-16877788;