rs16976490

Variant names:

• chr17-71245906-T-C
• rs16976490

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 0.103 in 152,224 control chromosomes in the GnomAD database, including 1,009 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 0.10 (1009 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.42
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.189 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: 0.103 AC: 15669 AN: 152106 Hom.: 1009 Cov.: 33

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0728

Gnomad ASJ AF: 0.0882

Gnomad EAS AF: 0.0894

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0641

Gnomad OTH AF: 0.0888

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

GnomAD4 genome AF: 0.103 AC: 15684 AN: 152224 Hom.: 1009 Cov.: 33 AF XY: 0.107 AC XY: 7997 AN XY: 74426

African (AFR) AF: 0.166 AC: 6885 AN: 41520

American (AMR) AF: 0.0727 AC: 1113 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0882 AC: 306 AN: 3470

East Asian (EAS) AF: 0.0898 AC: 465 AN: 5176

South Asian (SAS) AF: 0.200 AC: 963 AN: 4822

European-Finnish (FIN) AF: 0.126 AC: 1334 AN: 10604

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0641 AC: 4362 AN: 68008

Other (OTH) AF: 0.0893 AC: 189 AN: 2116

Alfa AF: 0.0809 Hom.: 327

Bravo AF: 0.0979

Asia WGS AF: 0.171 AC: 593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.9
DANN	Benign	0.42
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs16976490; hg19: chr17-69242047;