rs2581226

Variant names:

• chr2-192275657-G-A
• rs2581226

Your query was ambiguous. Multiple possible variants found:

• chr2-192275657-G-A
• chr2-192275657-G-C

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 0.819 in 150,816 control chromosomes in the GnomAD database, including 50,977 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 0.82 (50977 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.218

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.891 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: 0.819 AC: 123406 AN: 150696 Hom.: 50936 Cov.: 26

Gnomad AFR AF: 0.898

Gnomad AMI AF: 0.881

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.758

Gnomad NFE AF: 0.813

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.819 AC: 123504 AN: 150816 Hom.: 50977 Cov.: 26 AF XY: 0.816 AC XY: 60032 AN XY: 73568

Gnomad4 AFR AF: 0.898

Gnomad4 AMR AF: 0.767

Gnomad4 ASJ AF: 0.792

Gnomad4 EAS AF: 0.500

Gnomad4 SAS AF: 0.808

Gnomad4 FIN AF: 0.792

Gnomad4 NFE AF: 0.813

Gnomad4 OTH AF: 0.790

Alfa AF: 0.822 Hom.: 6032

Bravo AF: 0.814

Asia WGS AF: 0.717 AC: 2493 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.0
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2581226; hg19: chr2-193140383;