rs586586

Variant names:

• chr7-126129532-A-G
• rs586586

Your query was ambiguous. Multiple possible variants found:

• chr7-126129532-A-G
• chr7-126129532-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 0.736 in 151,618 control chromosomes in the GnomAD database, including 42,157 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 (42157 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.304
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.736 AC: 111499 AN: 151500 Hom.: 42141 Cov.: 31

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.817

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.736 AC: 111544 AN: 151618 Hom.: 42157 Cov.: 31 AF XY: 0.736 AC XY: 54549 AN XY: 74112

African (AFR) AF: 0.549 AC: 22721 AN: 41402

American (AMR) AF: 0.823 AC: 12467 AN: 15154

Ashkenazi Jewish (ASJ) AF: 0.843 AC: 2922 AN: 3466

East Asian (EAS) AF: 0.681 AC: 3513 AN: 5156

South Asian (SAS) AF: 0.814 AC: 3927 AN: 4826

European-Finnish (FIN) AF: 0.785 AC: 8265 AN: 10532

Middle Eastern (MID) AF: 0.817 AC: 237 AN: 290

European-Non Finnish (NFE) AF: 0.814 AC: 55190 AN: 67778

Other (OTH) AF: 0.773 AC: 1627 AN: 2106

Alfa AF: 0.708 Hom.: 2273

Bravo AF: 0.731

Asia WGS AF: 0.692 AC: 2377 AN: 3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	6.0
DANN	Benign	0.89
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs586586; hg19: chr7-125769586;