chr2-133886525-C-T

Variant names:

• chr2-133886525-C-T
• rs6711228

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 0.102 in 151,984 control chromosomes in the GnomAD database, including 881 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 0.10 (881 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.666
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.157 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: 0.101 AC: 15408 AN: 151866 Hom.: 879 Cov.: 32

Gnomad AFR AF: 0.0623

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.102 AC: 15436 AN: 151984 Hom.: 881 Cov.: 32 AF XY: 0.104 AC XY: 7755 AN XY: 74296

African (AFR) AF: 0.0625 AC: 2591 AN: 41432

American (AMR) AF: 0.152 AC: 2320 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 523 AN: 3472

East Asian (EAS) AF: 0.166 AC: 854 AN: 5152

South Asian (SAS) AF: 0.147 AC: 708 AN: 4810

European-Finnish (FIN) AF: 0.115 AC: 1214 AN: 10534

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6906 AN: 67986

Other (OTH) AF: 0.121 AC: 256 AN: 2112

Alfa AF: 0.108 Hom.: 1732

Bravo AF: 0.104

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.27
DANN	Benign	0.63
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs6711228; hg19: chr2-134644096;