rs16976482

Variant names:

• chr17-71241387-C-T
• rs16976482

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 0.198 in 152,122 control chromosomes in the GnomAD database, including 5,252 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 0.20 (5252 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.775
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.462 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: 0.198 AC: 30076 AN: 152002 Hom.: 5236 Cov.: 32

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.0920

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.0750

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.198 AC: 30127 AN: 152122 Hom.: 5252 Cov.: 32 AF XY: 0.199 AC XY: 14784 AN XY: 74382

African (AFR) AF: 0.468 AC: 19398 AN: 41454

American (AMR) AF: 0.118 AC: 1807 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 448 AN: 3472

East Asian (EAS) AF: 0.0922 AC: 478 AN: 5182

South Asian (SAS) AF: 0.209 AC: 1009 AN: 4818

European-Finnish (FIN) AF: 0.137 AC: 1454 AN: 10592

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0750 AC: 5103 AN: 68008

Other (OTH) AF: 0.168 AC: 355 AN: 2110

Alfa AF: 0.157 Hom.: 607

Bravo AF: 0.205

Asia WGS AF: 0.216 AC: 749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	14
DANN	Benign	0.50
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs16976482; hg19: chr17-69237528;