chr2-32053713-A-G

Variant names:

• chr2-32053713-A-G
• rs7577696

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 0.423 in 151,870 control chromosomes in the GnomAD database, including 13,867 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 0.42 (13867 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.608
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.624 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: 0.423 AC: 64163 AN: 151752 Hom.: 13850 Cov.: 31

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.423 AC: 64222 AN: 151870 Hom.: 13867 Cov.: 31 AF XY: 0.424 AC XY: 31515 AN XY: 74248

African (AFR) AF: 0.423 AC: 17495 AN: 41400

American (AMR) AF: 0.422 AC: 6423 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1778 AN: 3466

East Asian (EAS) AF: 0.643 AC: 3324 AN: 5172

South Asian (SAS) AF: 0.557 AC: 2684 AN: 4816

European-Finnish (FIN) AF: 0.368 AC: 3874 AN: 10532

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27229 AN: 67966

Other (OTH) AF: 0.428 AC: 901 AN: 2104

Alfa AF: 0.415 Hom.: 55376

Bravo AF: 0.428

Asia WGS AF: 0.623 AC: 2161 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.46
DANN	Benign	0.28
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs7577696; hg19: chr2-32278782;