13-52823429-G-T

Variant names:

• chr13-52823429-G-T
• rs622348
• ENST00000809893.1:n.336-26325G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000809893.1(ENSG00000305264):​n.336-26325G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.633 in 151,950 control chromosomes in the GnomAD database, including 30,533 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 0.63 (30533 hom., cov: 32)
• Consequence: ENSG00000305264 ENST00000809893.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.150
• Publications: 3 publications found

Genes affected

ENSG00000305264 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.674 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
ENSG00000305264	ENST00000809893.1	n.336-26325G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96073 AN: 151832 Hom.: 30520 Cov.: 32

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.633 AC: 96131 AN: 151950 Hom.: 30533 Cov.: 32 AF XY: 0.628 AC XY: 46621 AN XY: 74256

African (AFR) AF: 0.681 AC: 28198 AN: 41428

American (AMR) AF: 0.609 AC: 9298 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1870 AN: 3470

East Asian (EAS) AF: 0.666 AC: 3434 AN: 5156

South Asian (SAS) AF: 0.567 AC: 2723 AN: 4802

European-Finnish (FIN) AF: 0.604 AC: 6372 AN: 10548

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.625 AC: 42486 AN: 67962

Other (OTH) AF: 0.588 AC: 1239 AN: 2108

Alfa AF: 0.619 Hom.: 47833

Bravo AF: 0.635

Asia WGS AF: 0.604 AC: 2105 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	2.9
DANN	Benign	0.64
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs622348; hg19: chr13-53397564;