rs2034586

Variant names:

• chr5-30046380-G-A
• rs2034586

Your query was ambiguous. Multiple possible variants found:

• chr5-30046380-G-A
• chr5-30046380-G-C
• chr5-30046380-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 0.405 in 151,982 control chromosomes in the GnomAD database, including 13,119 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 0.40 (13119 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0840
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.757 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: 0.405 AC: 61451 AN: 151864 Hom.: 13098 Cov.: 33

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.346

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.405 AC: 61512 AN: 151982 Hom.: 13119 Cov.: 33 AF XY: 0.411 AC XY: 30540 AN XY: 74282

African (AFR) AF: 0.366 AC: 15183 AN: 41428

American (AMR) AF: 0.472 AC: 7208 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1312 AN: 3470

East Asian (EAS) AF: 0.777 AC: 4015 AN: 5166

South Asian (SAS) AF: 0.580 AC: 2796 AN: 4822

European-Finnish (FIN) AF: 0.393 AC: 4146 AN: 10556

Middle Eastern (MID) AF: 0.338 AC: 98 AN: 290

European-Non Finnish (NFE) AF: 0.376 AC: 25564 AN: 67956

Other (OTH) AF: 0.402 AC: 847 AN: 2108

Alfa AF: 0.317 Hom.: 1501

Bravo AF: 0.404

Asia WGS AF: 0.697 AC: 2418 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.6
DANN	Benign	0.40
PhyloP100		0.084

Splicing

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

Other links and lift over

dbSNP: rs2034586; hg19: chr5-30046487;