chr13-28592262-G-A

Variant names:

• chr13-28592262-G-A
• rs17086849
• ENST00000784142.1:n.527-596C>T

Variant summary

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

The ENST00000784142.1(ENSG00000289569):​n.527-596C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 151,226 control chromosomes in the GnomAD database, including 5,348 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 0.25 (5348 hom., cov: 28)
• Consequence: ENSG00000289569 ENST00000784142.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.323
• Publications: 8 publications found

Genes affected

ENSG00000289569 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 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
ENSG00000289569	ENST00000784142.1	n.527-596C>T		intron_variant	Intron 4 of 4
ENSG00000289569	ENST00000784143.1	n.519-596C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.251 AC: 37979 AN: 151106 Hom.: 5347 Cov.: 28

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.202

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.251 AC: 38019 AN: 151226 Hom.: 5348 Cov.: 28 AF XY: 0.252 AC XY: 18640 AN XY: 73850

African (AFR) AF: 0.359 AC: 14736 AN: 41090

American (AMR) AF: 0.298 AC: 4525 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 640 AN: 3466

East Asian (EAS) AF: 0.288 AC: 1462 AN: 5084

South Asian (SAS) AF: 0.337 AC: 1606 AN: 4770

European-Finnish (FIN) AF: 0.154 AC: 1612 AN: 10496

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.187 AC: 12697 AN: 67852

Other (OTH) AF: 0.229 AC: 482 AN: 2108

Alfa AF: 0.196 Hom.: 1946

Bravo AF: 0.269

Asia WGS AF: 0.310 AC: 1079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.9
DANN	Benign	0.81
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs17086849; hg19: chr13-29166399;