13-53413033-A-G

Position:

• chr13-53413033-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.764 in 151,784 control chromosomes in the GnomAD database, including 45,493 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 0.76 (45493 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.93

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.53413033A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287722	ENST00000657016.1	n.629+108911A>G		intron_variant
ENSG00000288768	ENST00000688155.1	n.46-9747A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.765 AC: 115963 AN: 151668 Hom.: 45479 Cov.: 30

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.817

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.956

Gnomad SAS AF: 0.895

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.790

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

GnomAD4 genome AF: 0.764 AC: 116020 AN: 151784 Hom.: 45493 Cov.: 30 AF XY: 0.767 AC XY: 56884 AN XY: 74154

Gnomad4 AFR AF: 0.564

Gnomad4 AMR AF: 0.803

Gnomad4 ASJ AF: 0.844

Gnomad4 EAS AF: 0.956

Gnomad4 SAS AF: 0.895

Gnomad4 FIN AF: 0.822

Gnomad4 NFE AF: 0.839

Gnomad4 OTH AF: 0.789

Alfa AF: 0.797 Hom.: 6104

Bravo AF: 0.751

Asia WGS AF: 0.886 AC: 3079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.054
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2053605; hg19: chr13-53987168;