rs4586493

Variant names:

• chr17-50847104-A-G
• rs4586493

Your query was ambiguous. Multiple possible variants found:

• chr17-50847104-A-G
• chr17-50847104-A-T

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 0.674 in 151,752 control chromosomes in the GnomAD database, including 34,684 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 0.67 (34684 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.713 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: 0.674 AC: 102138 AN: 151636 Hom.: 34641 Cov.: 29

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.674 AC: 102239 AN: 151752 Hom.: 34684 Cov.: 29 AF XY: 0.667 AC XY: 49475 AN XY: 74170

African (AFR) AF: 0.654 AC: 27035 AN: 41310

American (AMR) AF: 0.581 AC: 8846 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.718 AC: 2489 AN: 3466

East Asian (EAS) AF: 0.436 AC: 2242 AN: 5144

South Asian (SAS) AF: 0.690 AC: 3309 AN: 4796

European-Finnish (FIN) AF: 0.681 AC: 7180 AN: 10544

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.719 AC: 48836 AN: 67940

Other (OTH) AF: 0.685 AC: 1443 AN: 2108

Alfa AF: 0.700 Hom.: 120577

Bravo AF: 0.657

Asia WGS AF: 0.601 AC: 2086 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.15
DANN	Benign	0.48
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs4586493; hg19: chr17-48924465;