rs17266958

Variant names:

• chr9-80650334-C-T
• rs17266958

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 0.0655 in 152,046 control chromosomes in the GnomAD database, including 398 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 0.066 (398 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.421
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.148 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: 0.0656 AC: 9960 AN: 151928 Hom.: 398 Cov.: 32

Gnomad AFR AF: 0.0391

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.0515

Gnomad ASJ AF: 0.0897

Gnomad EAS AF: 0.0309

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.0778

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.0761

Gnomad OTH AF: 0.0666

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

GnomAD4 genome AF: 0.0655 AC: 9963 AN: 152046 Hom.: 398 Cov.: 32 AF XY: 0.0671 AC XY: 4986 AN XY: 74330

African (AFR) AF: 0.0392 AC: 1627 AN: 41484

American (AMR) AF: 0.0514 AC: 783 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.0897 AC: 311 AN: 3466

East Asian (EAS) AF: 0.0304 AC: 157 AN: 5164

South Asian (SAS) AF: 0.157 AC: 758 AN: 4814

European-Finnish (FIN) AF: 0.0778 AC: 825 AN: 10602

Middle Eastern (MID) AF: 0.0856 AC: 25 AN: 292

European-Non Finnish (NFE) AF: 0.0761 AC: 5174 AN: 67958

Other (OTH) AF: 0.0669 AC: 141 AN: 2108

Alfa AF: 0.0631 Hom.: 52

Bravo AF: 0.0594

Asia WGS AF: 0.109 AC: 376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.40
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs17266958; hg19: chr9-83265249;