rs10962668

Positions:

• chr9-16894142-T-C

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 0.437 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.474

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.428

Alfa AF: 0.512 Hom.: 5713

Bravo AF: 0.416

Asia WGS AF: 0.228 AC: 793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10962668; hg19: chr9-16894140;