2-237127724-C-T

Variant names:

• chr2-237127724-C-T
• rs12620999

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 0.706 in 152,190 control chromosomes in the GnomAD database, including 41,083 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 0.71 (41083 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.354
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 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: 0.707 AC: 107483 AN: 152072 Hom.: 41081 Cov.: 34

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.809

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.732

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

GnomAD4 genome AF: 0.706 AC: 107512 AN: 152190 Hom.: 41083 Cov.: 34 AF XY: 0.714 AC XY: 53161 AN XY: 74412

African (AFR) AF: 0.389 AC: 16127 AN: 41478

American (AMR) AF: 0.840 AC: 12849 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.809 AC: 2808 AN: 3470

East Asian (EAS) AF: 0.979 AC: 5074 AN: 5184

South Asian (SAS) AF: 0.883 AC: 4256 AN: 4822

European-Finnish (FIN) AF: 0.819 AC: 8688 AN: 10608

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.811 AC: 55162 AN: 68014

Other (OTH) AF: 0.734 AC: 1548 AN: 2108

Alfa AF: 0.797 Hom.: 39687

Bravo AF: 0.693

Asia WGS AF: 0.886 AC: 3082 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.71
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs12620999; hg19: chr2-238036367;