rs16976482

Variant names:

• chr17-71241387-C-T
• rs16976482

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 0.198 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.468

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.0922

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.0750

Gnomad4 OTH AF: 0.168

Alfa AF: 0.147 Hom.: 525

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16976482; hg19: chr17-69237528;