rs17708876

Variant names:

• chr16-31387145-T-C
• rs17708876

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 0.134 in 152,228 control chromosomes in the GnomAD database, including 1,545 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 0.13 (1545 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20359 AN: 152110 Hom.: 1549 Cov.: 33

Gnomad AFR AF: 0.0834

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.0896

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.0408

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.134 AC: 20357 AN: 152228 Hom.: 1545 Cov.: 33 AF XY: 0.133 AC XY: 9927 AN XY: 74440

African (AFR) AF: 0.0834 AC: 3464 AN: 41530

American (AMR) AF: 0.0895 AC: 1369 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 401 AN: 3468

East Asian (EAS) AF: 0.0407 AC: 211 AN: 5188

South Asian (SAS) AF: 0.120 AC: 582 AN: 4830

European-Finnish (FIN) AF: 0.218 AC: 2306 AN: 10592

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11453 AN: 68012

Other (OTH) AF: 0.123 AC: 260 AN: 2110

Alfa AF: 0.149 Hom.: 2309

Bravo AF: 0.122

Asia WGS AF: 0.101 AC: 350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.26
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs17708876; hg19: chr16-31398466;