rs13242133

Variant names:

• chr7-1249643-G-A
• rs13242133

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 0.684 in 148,758 control chromosomes in the GnomAD database, including 36,489 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 0.68 (36489 hom., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300
• Publications: 4 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 (SAS) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.684 AC: 101649 AN: 148640 Hom.: 36481 Cov.: 22

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.684 AC: 101687 AN: 148758 Hom.: 36489 Cov.: 22 AF XY: 0.685 AC XY: 49615 AN XY: 72400

African (AFR) AF: 0.459 AC: 18459 AN: 40248

American (AMR) AF: 0.668 AC: 10030 AN: 15018

Ashkenazi Jewish (ASJ) AF: 0.773 AC: 2667 AN: 3452

East Asian (EAS) AF: 0.706 AC: 3470 AN: 4916

South Asian (SAS) AF: 0.836 AC: 3871 AN: 4628

European-Finnish (FIN) AF: 0.772 AC: 7725 AN: 10006

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.792 AC: 53292 AN: 67246

Other (OTH) AF: 0.700 AC: 1433 AN: 2048

Alfa AF: 0.764 Hom.: 45098

Bravo AF: 0.662

Asia WGS AF: 0.777 AC: 2700 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.7
DANN	Benign	0.22
PhyloP100		0.0030

Splicing

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

Other links and lift over

dbSNP: rs13242133; hg19: chr7-1289279;