2-226275057-C-T

Variant names:

• chr2-226275057-C-T
• rs10167219

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 0.247 in 151,858 control chromosomes in the GnomAD database, including 5,841 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 0.25 (5841 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.434 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: 0.246 AC: 37401 AN: 151740 Hom.: 5824 Cov.: 32

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.247 AC: 37469 AN: 151858 Hom.: 5841 Cov.: 32 AF XY: 0.247 AC XY: 18338 AN XY: 74226

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.215

Alfa AF: 0.0993 Hom.: 156

Bravo AF: 0.259

Asia WGS AF: 0.410 AC: 1423 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.090
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10167219; hg19: chr2-227139773;