rs2532087

Variant names:

• chr4-15876704-C-G
• rs2532087

Your query was ambiguous. Multiple possible variants found:

• chr4-15876704-C-G
• chr4-15876704-C-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 0.831 in 152,220 control chromosomes in the GnomAD database, including 53,136 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 0.83 (53136 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.944 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: 0.831 AC: 126456 AN: 152102 Hom.: 53083 Cov.: 32

Gnomad AFR AF: 0.952

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.813

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

GnomAD4 genome AF: 0.831 AC: 126565 AN: 152220 Hom.: 53136 Cov.: 32 AF XY: 0.825 AC XY: 61434 AN XY: 74422

African (AFR) AF: 0.952 AC: 39535 AN: 41544

American (AMR) AF: 0.764 AC: 11682 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.743 AC: 2578 AN: 3472

East Asian (EAS) AF: 0.620 AC: 3208 AN: 5174

South Asian (SAS) AF: 0.703 AC: 3388 AN: 4818

European-Finnish (FIN) AF: 0.788 AC: 8343 AN: 10590

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.810 AC: 55119 AN: 68008

Other (OTH) AF: 0.808 AC: 1710 AN: 2116

Alfa AF: 0.839 Hom.: 6285

Bravo AF: 0.835

Asia WGS AF: 0.687 AC: 2394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.84
DANN	Benign	0.57
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs2532087; hg19: chr4-15878327;