Variant 13-40789459-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000478827.1(SLC25A15):n.48T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 151,382 control chromosomes in the GnomAD database, including 24,189 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.56 ( 24182 hom., cov: 34)

Exomes 𝑓: 0.33 ( 7 hom. )

Consequence

SLC25A15
ENST00000478827.1 non_coding_transcript_exon

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.152

Variant links:

Genes affected

SLC25A15 (HGNC:):

SLC25A15 links:

SLC25A15 (HGNC:10985): (solute carrier family 25 member 15) This gene is a member of the mitochondrial carrier family. The encoded protein transports ornithine across the inner mitochondrial membrane from the cytosol to the mitochondrial matrix. The protein is an essential component of the urea cycle, and functions in ammonium detoxification and biosynthesis of the amino acid arginine. Mutations in this gene result in hyperornithinemia-hyperammonemia-homocitrullinuria (HHH) syndrome. There is a pseudogene of this locus on the Y chromosome.[provided by RefSeq, May 2009]

SLC25A15 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BP6

Variant 13-40789459-T-C is Benign according to our data. Variant chr13-40789459-T-C is described in ClinVar as [Benign]. Clinvar id is 312168.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.40789459T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC25A15	ENST00000478827.1 linkuse as main transcript	n.48T>C		non_coding_transcript_exon_variant	1/7	5
SLC25A15	ENST00000707033.1 linkuse as main transcript	c.-274T>C		upstream_gene_variant				ENSP00000516711.1		Q9Y619

Frequencies

GnomAD3 genomes

AF:

0.562

AC:

84988

AN:

151164

Hom.:

24144

Cov.:

show subpopulations

Gnomad AFR

AF:

0.630

Gnomad AMI

AF:

0.663

Gnomad AMR

AF:

0.602

Gnomad ASJ

AF:

0.579

Gnomad EAS

AF:

0.584

Gnomad SAS

AF:

0.486

Gnomad FIN

AF:

0.579

Gnomad MID

AF:

0.653

Gnomad NFE

AF:

0.509

Gnomad OTH

AF:

0.595

GnomAD4 exome

AF:

0.327

AC:

AN:

110

Hom.:

Cov.:

AF XY:

0.341

AC XY:

AN XY:

show subpopulations

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.500

Gnomad4 SAS exome

AF:

0.500

Gnomad4 FIN exome

AF:

1.00

Gnomad4 NFE exome

AF:

0.298

GnomAD4 genome

AF:

0.562

AC:

85078

AN:

151272

Hom.:

24182

Cov.:

AF XY:

0.566

AC XY:

41821

AN XY:

73908

show subpopulations

Gnomad4 AFR

AF:

0.631

Gnomad4 AMR

AF:

0.602

Gnomad4 ASJ

AF:

0.579

Gnomad4 EAS

AF:

0.584

Gnomad4 SAS

AF:

0.483

Gnomad4 FIN

AF:

0.579

Gnomad4 NFE

AF:

0.509

Gnomad4 OTH

AF:

0.597

Alfa

AF:

0.377

Hom.:

923

Bravo

AF:

0.570

Asia WGS

AF:

0.557

AC:

1860

AN:

3338

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 29, 2018	- -

Hyperornithinemia-hyperammonemia-homocitrullinuria syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

7.4

DANN

Benign

0.17

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over