rs2741270

Variant names:

• chr2-232464717-C-T
• rs2741270

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.163 AC: 6768 AN: 41540

American (AMR) AF: 0.106 AC: 1622 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 434 AN: 3470

East Asian (EAS) AF: 0.248 AC: 1283 AN: 5168

South Asian (SAS) AF: 0.154 AC: 742 AN: 4818

European-Finnish (FIN) AF: 0.146 AC: 1546 AN: 10606

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8003 AN: 68022

Other (OTH) AF: 0.129 AC: 273 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.087
DANN	Benign	0.35
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs2741270; hg19: chr2-233329427;