rs10962668

Variant names:

• chr9-16894142-T-C
• rs10962668

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 0.437 in 151,954 control chromosomes in the GnomAD database, including 16,870 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 0.44 (16870 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66424 AN: 151836 Hom.: 16866 Cov.: 31

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.437 AC: 66450 AN: 151954 Hom.: 16870 Cov.: 31 AF XY: 0.431 AC XY: 32006 AN XY: 74286

African (AFR) AF: 0.224 AC: 9279 AN: 41418

American (AMR) AF: 0.372 AC: 5677 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1645 AN: 3468

East Asian (EAS) AF: 0.223 AC: 1149 AN: 5162

South Asian (SAS) AF: 0.222 AC: 1071 AN: 4816

European-Finnish (FIN) AF: 0.582 AC: 6145 AN: 10566

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.590 AC: 40094 AN: 67962

Other (OTH) AF: 0.428 AC: 903 AN: 2108

Alfa AF: 0.537 Hom.: 10822

Bravo AF: 0.416

Asia WGS AF: 0.228 AC: 793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.7
DANN	Benign	0.79
PhyloP100		0.036

Splicing

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

Other links and lift over

dbSNP: rs10962668; hg19: chr9-16894140;