rs17066662

Variant names:

• chr6-137639876-C-T
• rs17066662

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.241 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

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.0953

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.243

Alfa AF: 0.261 Hom.: 1971

Bravo AF: 0.247

Asia WGS AF: 0.156 AC: 543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17066662; hg19: chr6-137961013;