chr17-13221732-T-C

Variant names:

• chr17-13221732-T-C
• rs971718

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 0.0615 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0615 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

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.0272

Gnomad4 ASJ AF: 0.0516

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.0848

Gnomad4 FIN AF: 0.0315

Gnomad4 NFE AF: 0.0337

Gnomad4 OTH AF: 0.0501

Alfa AF: 0.0389 Hom.: 135

Bravo AF: 0.0639

Asia WGS AF: 0.145 AC: 503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs971718; hg19: chr17-13125049;