rs1584586

Variant names:

• chr3-150476564-G-A
• rs1584586

Your query was ambiguous. Multiple possible variants found:

• chr3-150476564-G-A
• chr3-150476564-G-C
• chr3-150476564-G-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 0.253 in 152,014 control chromosomes in the GnomAD database, including 5,348 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 0.25 (5348 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.344 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: 0.253 AC: 38446 AN: 151896 Hom.: 5343 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.253 AC: 38471 AN: 152014 Hom.: 5348 Cov.: 32 AF XY: 0.253 AC XY: 18785 AN XY: 74324

African (AFR) AF: 0.151 AC: 6284 AN: 41486

American (AMR) AF: 0.235 AC: 3591 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 536 AN: 3470

East Asian (EAS) AF: 0.358 AC: 1853 AN: 5176

South Asian (SAS) AF: 0.255 AC: 1229 AN: 4820

European-Finnish (FIN) AF: 0.274 AC: 2881 AN: 10524

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21307 AN: 67934

Other (OTH) AF: 0.232 AC: 490 AN: 2116

Alfa AF: 0.272 Hom.: 4034

Bravo AF: 0.246

Asia WGS AF: 0.300 AC: 1040 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	12
DANN	Benign	0.61
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs1584586; hg19: chr3-150194351;