ENST00000560360.2:n.313+83131C>T

Variant names:

• chr15-98174448-G-A
• rs1383139
• ENST00000560360.2:n.313+83131C>T

Variant summary

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

The ENST00000560360.2(ENSG00000259199):​n.313+83131C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 151,902 control chromosomes in the GnomAD database, including 21,303 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 0.53 (21303 hom., cov: 31)
• Consequence: ENSG00000259199 ENST00000560360.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.816
• Publications: 5 publications found

Genes affected

ENSG00000259199 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.661 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
ENSG00000259199	ENST00000560360.2	n.313+83131C>T		intron_variant	Intron 3 of 4	5
ENSG00000259199	ENST00000717124.1	n.291+83131C>T		intron_variant	Intron 3 of 8
ENSG00000305856	ENST00000813524.1	n.71+3651C>T		intron_variant	Intron 1 of 4
ENSG00000305856	ENST00000813525.1	n.145+3651C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80201 AN: 151784 Hom.: 21291 Cov.: 31

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.528 AC: 80242 AN: 151902 Hom.: 21303 Cov.: 31 AF XY: 0.528 AC XY: 39173 AN XY: 74238

African (AFR) AF: 0.540 AC: 22348 AN: 41422

American (AMR) AF: 0.590 AC: 9006 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1614 AN: 3464

East Asian (EAS) AF: 0.679 AC: 3498 AN: 5148

South Asian (SAS) AF: 0.510 AC: 2452 AN: 4812

European-Finnish (FIN) AF: 0.480 AC: 5059 AN: 10546

Middle Eastern (MID) AF: 0.479 AC: 139 AN: 290

European-Non Finnish (NFE) AF: 0.508 AC: 34501 AN: 67926

Other (OTH) AF: 0.534 AC: 1126 AN: 2110

Alfa AF: 0.490 Hom.: 8486

Bravo AF: 0.540

Asia WGS AF: 0.549 AC: 1907 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.69
DANN	Benign	0.64
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs1383139; hg19: chr15-98717677;