2-133887223-T-C

Variant names:

• chr2-133887223-T-C
• rs7582472

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 0.21 in 152,170 control chromosomes in the GnomAD database, including 3,386 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 0.21 (3386 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31897 AN: 152052 Hom.: 3385 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.210 AC: 31925 AN: 152170 Hom.: 3386 Cov.: 32 AF XY: 0.214 AC XY: 15909 AN XY: 74392

African (AFR) AF: 0.191 AC: 7935 AN: 41496

American (AMR) AF: 0.253 AC: 3874 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 890 AN: 3470

East Asian (EAS) AF: 0.253 AC: 1309 AN: 5166

South Asian (SAS) AF: 0.274 AC: 1319 AN: 4818

European-Finnish (FIN) AF: 0.229 AC: 2420 AN: 10588

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13500 AN: 68018

Other (OTH) AF: 0.222 AC: 470 AN: 2114

Alfa AF: 0.213 Hom.: 3089

Bravo AF: 0.212

Asia WGS AF: 0.267 AC: 927 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	12
DANN	Benign	0.52
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs7582472; hg19: chr2-134644794;