chr17-31543954-G-T

Variant names:

• chr17-31543954-G-T
• rs739630

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 0.738 in 152,200 control chromosomes in the GnomAD database, including 42,048 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 0.74 (42048 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.866 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: 0.738 AC: 112259 AN: 152082 Hom.: 41996 Cov.: 34

Gnomad AFR AF: 0.874

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.738 AC: 112361 AN: 152200 Hom.: 42048 Cov.: 34 AF XY: 0.732 AC XY: 54497 AN XY: 74404

African (AFR) AF: 0.874 AC: 36310 AN: 41544

American (AMR) AF: 0.607 AC: 9288 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.746 AC: 2588 AN: 3470

East Asian (EAS) AF: 0.771 AC: 3989 AN: 5176

South Asian (SAS) AF: 0.615 AC: 2966 AN: 4824

European-Finnish (FIN) AF: 0.710 AC: 7514 AN: 10580

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.695 AC: 47230 AN: 68004

Other (OTH) AF: 0.744 AC: 1569 AN: 2108

Alfa AF: 0.706 Hom.: 63943

Bravo AF: 0.737

Asia WGS AF: 0.706 AC: 2454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	8.3
DANN	Benign	0.79
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs739630; hg19: chr17-29870973;