rs2741270

chr2-232464717-C-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 0.136 in 152,244 control chromosomes in the GnomAD database, including 1,464 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 0.14 (1464 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.76

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.237 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: 0.137 AC: 20769 AN: 152126 Hom.: 1465 Cov.: 33

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.136 AC: 20774 AN: 152244 Hom.: 1464 Cov.: 33 AF XY: 0.137 AC XY: 10229 AN XY: 74424

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.129

Alfa AF: 0.130 Hom.: 151

Bravo AF: 0.134

Asia WGS AF: 0.156 AC: 543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.087
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2741270; hg19: chr2-233329427;