chr17-31796958-G-A

Variant names:

• chr17-31796958-G-A
• rs757288

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 0.782 in 152,070 control chromosomes in the GnomAD database, including 46,540 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 0.78 (46540 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.208
• 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 (AFR) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.782 AC: 118780 AN: 151952 Hom.: 46503 Cov.: 31

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.763

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.782 AC: 118873 AN: 152070 Hom.: 46540 Cov.: 31 AF XY: 0.784 AC XY: 58287 AN XY: 74324

African (AFR) AF: 0.796 AC: 33017 AN: 41490

American (AMR) AF: 0.769 AC: 11749 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.707 AC: 2453 AN: 3470

East Asian (EAS) AF: 0.763 AC: 3944 AN: 5166

South Asian (SAS) AF: 0.769 AC: 3705 AN: 4820

European-Finnish (FIN) AF: 0.817 AC: 8620 AN: 10556

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.778 AC: 52870 AN: 67976

Other (OTH) AF: 0.763 AC: 1614 AN: 2114

Alfa AF: 0.773 Hom.: 28193

Bravo AF: 0.777

Asia WGS AF: 0.777 AC: 2704 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	2.2
DANN	Benign	0.49
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs757288; hg19: chr17-30123977;