13-53413033-A-G

Variant names:

• chr13-53413033-A-G
• rs2053605
• ENST00000657016.1:n.629+108911A>G

Variant summary

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

The ENST00000657016.1(ENSG00000287722):​n.629+108911A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000287722 ENST00000657016.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.93

Genes affected

ENSG00000287722 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287722	ENST00000657016.1	n.629+108911A>G		intron_variant	Intron 2 of 3
ENSG00000288768	ENST00000688155.1	n.46-9747A>G		intron_variant	Intron 1 of 2

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;