rs13329271

Variant names:

• chr15-78621888-A-C
• rs13329271
• ENST00000821537.1:n.210+1578A>C

Your query was ambiguous. Multiple possible variants found:

• chr15-78621888-A-C
• chr15-78621888-A-G
• chr15-78621888-A-T

Variant summary

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

The ENST00000821537.1(ENSG00000259555):​n.210+1578A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 152,006 control chromosomes in the GnomAD database, including 6,290 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 0.27 (6290 hom., cov: 32)
• Consequence: ENSG00000259555 ENST00000821537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.721
• Publications: 16 publications found

Genes affected

ENSG00000259555 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.448 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
ENSG00000259555	ENST00000821537.1	n.210+1578A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41287 AN: 151886 Hom.: 6269 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.272 AC: 41340 AN: 152006 Hom.: 6290 Cov.: 32 AF XY: 0.279 AC XY: 20715 AN XY: 74310

African (AFR) AF: 0.266 AC: 11031 AN: 41448

American (AMR) AF: 0.434 AC: 6631 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 780 AN: 3466

East Asian (EAS) AF: 0.463 AC: 2383 AN: 5142

South Asian (SAS) AF: 0.434 AC: 2089 AN: 4812

European-Finnish (FIN) AF: 0.271 AC: 2863 AN: 10572

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14728 AN: 67978

Other (OTH) AF: 0.283 AC: 598 AN: 2112

Alfa AF: 0.248 Hom.: 623

Bravo AF: 0.286

Asia WGS AF: 0.474 AC: 1646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.3
DANN	Benign	0.75
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs13329271; hg19: chr15-78914230;