chr17-58130370-A-G

Variant names:

• chr17-58130370-A-G
• rs181247

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 0.694 in 149,466 control chromosomes in the GnomAD database, including 38,883 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 0.69 (38883 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.475
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.882 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: 0.695 AC: 103749 AN: 149346 Hom.: 38871 Cov.: 29

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.705

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.694 AC: 103793 AN: 149466 Hom.: 38883 Cov.: 29 AF XY: 0.699 AC XY: 50945 AN XY: 72858

African (AFR) AF: 0.485 AC: 20013 AN: 41288

American (AMR) AF: 0.692 AC: 10334 AN: 14924

Ashkenazi Jewish (ASJ) AF: 0.752 AC: 2582 AN: 3434

East Asian (EAS) AF: 0.903 AC: 4678 AN: 5178

South Asian (SAS) AF: 0.843 AC: 4035 AN: 4788

European-Finnish (FIN) AF: 0.815 AC: 8001 AN: 9814

Middle Eastern (MID) AF: 0.686 AC: 199 AN: 290

European-Non Finnish (NFE) AF: 0.775 AC: 51773 AN: 66784

Other (OTH) AF: 0.715 AC: 1478 AN: 2068

Alfa AF: 0.744 Hom.: 27318

Asia WGS AF: 0.859 AC: 2983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.7
DANN	Benign	0.69
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs181247; hg19: chr17-56207731;