17-12317291-C-T

Variant names:

• chr17-12317291-C-T
• rs8077717

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 0.571 in 152,048 control chromosomes in the GnomAD database, including 28,012 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 0.57 (28012 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.394
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86836 AN: 151932 Hom.: 28017 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.571 AC: 86836 AN: 152048 Hom.: 28012 Cov.: 32 AF XY: 0.569 AC XY: 42284 AN XY: 74348

African (AFR) AF: 0.268 AC: 11115 AN: 41466

American (AMR) AF: 0.605 AC: 9244 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2350 AN: 3468

East Asian (EAS) AF: 0.322 AC: 1658 AN: 5152

South Asian (SAS) AF: 0.574 AC: 2770 AN: 4826

European-Finnish (FIN) AF: 0.758 AC: 8015 AN: 10568

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.729 AC: 49527 AN: 67978

Other (OTH) AF: 0.592 AC: 1251 AN: 2112

Alfa AF: 0.596 Hom.: 7192

Bravo AF: 0.548

Asia WGS AF: 0.449 AC: 1565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.42
DANN	Benign	0.22
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs8077717; hg19: chr17-12220608;