2-226257500-G-T

Position:

• chr2-226257500-G-T

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 0.642 in 151,898 control chromosomes in the GnomAD database, including 31,741 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 0.64 (31741 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 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: 0.641 AC: 97363 AN: 151780 Hom.: 31709 Cov.: 32

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.593

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.642 AC: 97453 AN: 151898 Hom.: 31741 Cov.: 32 AF XY: 0.643 AC XY: 47729 AN XY: 74208

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.731

Gnomad4 ASJ AF: 0.713

Gnomad4 EAS AF: 0.921

Gnomad4 SAS AF: 0.753

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.630

Gnomad4 OTH AF: 0.650

Alfa AF: 0.636 Hom.: 54705

Bravo AF: 0.648

Asia WGS AF: 0.829 AC: 2883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.60
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1515110; hg19: chr2-227122216;