rs2251692

chr2-226725064-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;