rs7342452

Variant names:

• chr13-22637805-G-A
• rs7342452

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 0.322 in 152,074 control chromosomes in the GnomAD database, including 12,023 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 0.32 (12023 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.234
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.689 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: 0.322 AC: 48883 AN: 151956 Hom.: 11971 Cov.: 32

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.322 AC: 48992 AN: 152074 Hom.: 12023 Cov.: 32 AF XY: 0.318 AC XY: 23643 AN XY: 74330

African (AFR) AF: 0.696 AC: 28830 AN: 41440

American (AMR) AF: 0.233 AC: 3568 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 517 AN: 3472

East Asian (EAS) AF: 0.274 AC: 1418 AN: 5180

South Asian (SAS) AF: 0.149 AC: 718 AN: 4820

European-Finnish (FIN) AF: 0.190 AC: 2011 AN: 10574

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11201 AN: 67988

Other (OTH) AF: 0.276 AC: 583 AN: 2112

Alfa AF: 0.263 Hom.: 1444

Bravo AF: 0.342

Asia WGS AF: 0.264 AC: 918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
DANN	Benign	0.54
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs7342452; hg19: chr13-23211944;