17-13221732-T-C

Variant names:

• chr17-13221732-T-C
• rs971718

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 0.0615 in 152,254 control chromosomes in the GnomAD database, including 422 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 0.062 (422 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.576
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.205 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: 0.0615 AC: 9360 AN: 152136 Hom.: 423 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.0272

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.0858

Gnomad FIN AF: 0.0315

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0336

Gnomad OTH AF: 0.0492

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

GnomAD4 genome AF: 0.0615 AC: 9368 AN: 152254 Hom.: 422 Cov.: 32 AF XY: 0.0625 AC XY: 4654 AN XY: 74440

African (AFR) AF: 0.106 AC: 4399 AN: 41526

American (AMR) AF: 0.0272 AC: 416 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0516 AC: 179 AN: 3468

East Asian (EAS) AF: 0.216 AC: 1118 AN: 5176

South Asian (SAS) AF: 0.0848 AC: 409 AN: 4822

European-Finnish (FIN) AF: 0.0315 AC: 334 AN: 10614

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0337 AC: 2290 AN: 68034

Other (OTH) AF: 0.0501 AC: 106 AN: 2116

Alfa AF: 0.0415 Hom.: 208

Bravo AF: 0.0639

Asia WGS AF: 0.145 AC: 503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.0
DANN	Benign	0.69
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs971718; hg19: chr17-13125049;