rs10810666

Variant names:

• chr9-16911668-C-T
• rs10810666

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.138 in 152,082 control chromosomes in the GnomAD database, including 1,816 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 0.14 (1816 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.202 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: 0.138 AC: 20935 AN: 151964 Hom.: 1815 Cov.: 32

Gnomad AFR AF: 0.0457

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0612

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.138 AC: 20941 AN: 152082 Hom.: 1816 Cov.: 32 AF XY: 0.134 AC XY: 9951 AN XY: 74354

Gnomad4 AFR AF: 0.0458

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0621

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.133

Alfa AF: 0.186 Hom.: 5605

Bravo AF: 0.128

Asia WGS AF: 0.0340 AC: 118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	15
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10810666; hg19: chr9-16911666; COSMIC: COSV60335683;