rs17066662

Variant names:

• chr6-137639876-C-T
• rs17066662

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 0.241 in 152,048 control chromosomes in the GnomAD database, including 4,619 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 0.24 (4619 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.63
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36593 AN: 151930 Hom.: 4615 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.0954

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.241 AC: 36597 AN: 152048 Hom.: 4619 Cov.: 32 AF XY: 0.239 AC XY: 17786 AN XY: 74340

African (AFR) AF: 0.188 AC: 7776 AN: 41472

American (AMR) AF: 0.290 AC: 4438 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1106 AN: 3470

East Asian (EAS) AF: 0.0953 AC: 493 AN: 5174

South Asian (SAS) AF: 0.257 AC: 1238 AN: 4818

European-Finnish (FIN) AF: 0.215 AC: 2267 AN: 10554

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18321 AN: 67964

Other (OTH) AF: 0.243 AC: 513 AN: 2114

Alfa AF: 0.259 Hom.: 2360

Bravo AF: 0.247

Asia WGS AF: 0.156 AC: 543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0040
DANN	Benign	0.87
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs17066662; hg19: chr6-137961013;