rs2082412

Variant names:

• chr5-159290781-G-A
• rs2082412

Your query was ambiguous. Multiple possible variants found:

• chr5-159290781-G-A
• chr5-159290781-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 0.274 in 152,118 control chromosomes in the GnomAD database, including 6,350 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 0.27 (6350 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.399
• Publications: 60 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.444 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: 0.274 AC: 41633 AN: 152000 Hom.: 6340 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.274 AC: 41669 AN: 152118 Hom.: 6350 Cov.: 32 AF XY: 0.277 AC XY: 20612 AN XY: 74372

African (AFR) AF: 0.371 AC: 15385 AN: 41476

American (AMR) AF: 0.339 AC: 5179 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 575 AN: 3468

East Asian (EAS) AF: 0.459 AC: 2374 AN: 5170

South Asian (SAS) AF: 0.363 AC: 1750 AN: 4826

European-Finnish (FIN) AF: 0.180 AC: 1905 AN: 10596

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13624 AN: 67980

Other (OTH) AF: 0.292 AC: 617 AN: 2116

Alfa AF: 0.236 Hom.: 15485

Bravo AF: 0.293

Asia WGS AF: 0.430 AC: 1492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.7
DANN	Benign	0.68
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs2082412; hg19: chr5-158717789;