rs726540

Variant names:

• chr13-52834269-T-G
• rs726540
• ENST00000809893.1:n.336-15485T>G

Variant summary

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

The ENST00000809893.1(ENSG00000305264):​n.336-15485T>G 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 152,018 control chromosomes in the GnomAD database, including 30,646 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 (30646 hom., cov: 32)
• Consequence: ENSG00000305264 ENST00000809893.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.213
• Publications: 7 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.776 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.336-15485T>G		intron_variant	Intron 2 of 2
ENSG00000305264	ENST00000809895.1	n.439+6900T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96130 AN: 151900 Hom.: 30623 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.633 AC: 96202 AN: 152018 Hom.: 30646 Cov.: 32 AF XY: 0.641 AC XY: 47630 AN XY: 74308

African (AFR) AF: 0.566 AC: 23431 AN: 41428

American (AMR) AF: 0.685 AC: 10458 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1974 AN: 3470

East Asian (EAS) AF: 0.796 AC: 4114 AN: 5168

South Asian (SAS) AF: 0.581 AC: 2797 AN: 4818

European-Finnish (FIN) AF: 0.752 AC: 7968 AN: 10590

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.637 AC: 43277 AN: 67964

Other (OTH) AF: 0.648 AC: 1367 AN: 2110

Alfa AF: 0.632 Hom.: 90322

Bravo AF: 0.627

Asia WGS AF: 0.688 AC: 2391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.1
DANN	Benign	0.74
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs726540; hg19: chr13-53408404;