rs2251692

Variant names:

• chr2-226725064-A-G
• rs2251692

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.697

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.578

Gnomad4 FIN AF: 0.708

Gnomad4 NFE AF: 0.748

Gnomad4 OTH AF: 0.582

Alfa AF: 0.701 Hom.: 89620

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2251692; hg19: chr2-227589780;