rs2251692

Variant names:

• chr2-226725064-A-G
• rs2251692

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 0.537 in 152,066 control chromosomes in the GnomAD database, including 27,250 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 0.54 (27250 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380
• Publications: 17 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 (NFE) allele frequency at 95% confidence interval = 0.743 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: 0.537 AC: 81670 AN: 151950 Hom.: 27257 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.537 AC: 81661 AN: 152066 Hom.: 27250 Cov.: 32 AF XY: 0.535 AC XY: 39802 AN XY: 74342

African (AFR) AF: 0.136 AC: 5641 AN: 41510

American (AMR) AF: 0.564 AC: 8616 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.697 AC: 2419 AN: 3472

East Asian (EAS) AF: 0.330 AC: 1698 AN: 5144

South Asian (SAS) AF: 0.578 AC: 2782 AN: 4814

European-Finnish (FIN) AF: 0.708 AC: 7475 AN: 10554

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.748 AC: 50860 AN: 67980

Other (OTH) AF: 0.582 AC: 1231 AN: 2114

Alfa AF: 0.674 Hom.: 127908

Bravo AF: 0.506

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.81
PhyloP100		0.038

Splicing

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

Other links and lift over

dbSNP: rs2251692; hg19: chr2-227589780;