rs1526687

Variant names:

• chr2-52486669-T-G
• rs1526687

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 0.203 in 152,016 control chromosomes in the GnomAD database, including 3,555 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 0.20 (3555 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.253 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: 0.203 AC: 30904 AN: 151898 Hom.: 3552 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.0121

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.203 AC: 30904 AN: 152016 Hom.: 3555 Cov.: 32 AF XY: 0.199 AC XY: 14749 AN XY: 74296

African (AFR) AF: 0.143 AC: 5924 AN: 41498

American (AMR) AF: 0.192 AC: 2921 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 587 AN: 3472

East Asian (EAS) AF: 0.0122 AC: 63 AN: 5174

South Asian (SAS) AF: 0.145 AC: 696 AN: 4810

European-Finnish (FIN) AF: 0.234 AC: 2478 AN: 10584

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17412 AN: 67932

Other (OTH) AF: 0.195 AC: 412 AN: 2112

Alfa AF: 0.198 Hom.: 1763

Bravo AF: 0.195

Asia WGS AF: 0.0960 AC: 334 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.57
PhyloP100		0.0080

Splicing

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

Other links and lift over

dbSNP: rs1526687; hg19: chr2-52713807;