2-133771520-G-A

Variant names:

• chr2-133771520-G-A
• rs6722456

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 0.0454 in 152,302 control chromosomes in the GnomAD database, including 248 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 0.045 (248 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282
• Publications: 14 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 = 0.147 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: 0.0454 AC: 6903 AN: 152184 Hom.: 248 Cov.: 33

Gnomad AFR AF: 0.0874

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0397

Gnomad ASJ AF: 0.0204

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.0234

Gnomad FIN AF: 0.00480

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0227

Gnomad OTH AF: 0.0334

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

GnomAD4 genome AF: 0.0454 AC: 6907 AN: 152302 Hom.: 248 Cov.: 33 AF XY: 0.0445 AC XY: 3313 AN XY: 74474

African (AFR) AF: 0.0873 AC: 3630 AN: 41560

American (AMR) AF: 0.0397 AC: 607 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0204 AC: 71 AN: 3472

East Asian (EAS) AF: 0.155 AC: 805 AN: 5178

South Asian (SAS) AF: 0.0238 AC: 115 AN: 4822

European-Finnish (FIN) AF: 0.00480 AC: 51 AN: 10618

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0227 AC: 1544 AN: 68032

Other (OTH) AF: 0.0331 AC: 70 AN: 2116

Alfa AF: 0.0363 Hom.: 267

Bravo AF: 0.0521

Asia WGS AF: 0.0810 AC: 280 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	3.0
DANN	Benign	0.21
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs6722456; hg19: chr2-134529091;