rs10810666

Variant names:

• chr9-16911668-C-T
• rs10810666

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0458 AC: 1899 AN: 41500

American (AMR) AF: 0.106 AC: 1623 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 764 AN: 3468

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5174

South Asian (SAS) AF: 0.0621 AC: 299 AN: 4814

European-Finnish (FIN) AF: 0.180 AC: 1900 AN: 10558

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13928 AN: 67976

Other (OTH) AF: 0.133 AC: 281 AN: 2112

Alfa AF: 0.176 Hom.: 8057

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
PhyloP100		1.4

Splicing

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

Other links and lift over

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