rs17706858

Variant names:

• chr6-135163956-C-T
• rs17706858

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 0.152 in 152,158 control chromosomes in the GnomAD database, including 1,890 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 0.15 (1890 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.182 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: 0.152 AC: 23055 AN: 152040 Hom.: 1894 Cov.: 32

Gnomad AFR AF: 0.0911

Gnomad AMI AF: 0.0736

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.152 AC: 23064 AN: 152158 Hom.: 1890 Cov.: 32 AF XY: 0.150 AC XY: 11186 AN XY: 74368

African (AFR) AF: 0.0911 AC: 3783 AN: 41504

American (AMR) AF: 0.146 AC: 2227 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 621 AN: 3470

East Asian (EAS) AF: 0.129 AC: 669 AN: 5184

South Asian (SAS) AF: 0.165 AC: 798 AN: 4822

European-Finnish (FIN) AF: 0.190 AC: 2008 AN: 10572

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12553 AN: 67990

Other (OTH) AF: 0.137 AC: 289 AN: 2114

Alfa AF: 0.166 Hom.: 653

Bravo AF: 0.145

Asia WGS AF: 0.143 AC: 496 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	11
DANN	Benign	0.67
PhyloP100		0.090

Splicing

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

Other links and lift over

dbSNP: rs17706858; hg19: chr6-135485094; COSMIC: COSV58836677;