2-236132153-G-A

Variant names:

• chr2-236132153-G-A
• rs6742722

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 0.286 in 152,020 control chromosomes in the GnomAD database, including 10,996 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 0.29 (10996 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43436 AN: 151902 Hom.: 10969 Cov.: 32

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.0279

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.286 AC: 43508 AN: 152020 Hom.: 10996 Cov.: 32 AF XY: 0.280 AC XY: 20810 AN XY: 74332

African (AFR) AF: 0.689 AC: 28549 AN: 41452

American (AMR) AF: 0.138 AC: 2116 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 448 AN: 3470

East Asian (EAS) AF: 0.0282 AC: 146 AN: 5186

South Asian (SAS) AF: 0.145 AC: 699 AN: 4820

European-Finnish (FIN) AF: 0.145 AC: 1530 AN: 10538

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9237 AN: 67962

Other (OTH) AF: 0.252 AC: 532 AN: 2110

Alfa AF: 0.171 Hom.: 6778

Bravo AF: 0.301

Asia WGS AF: 0.122 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.0060
DANN	Benign	0.69
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs6742722; hg19: chr2-237040797;