rs34615430

Variant names:

• chr13-40799183-G-A
• rs34615430
• NM_014252.4:c.182G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-40799183-G-A
• chr13-40799183-G-C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 3P and 13B. PM1 PP2 BP4_Strong BP6 BS1 BS2

The NM_014252.4(SLC25A15):​c.182G>A​(p.Arg61His) variant causes a missense change. The variant allele was found at a frequency of 0.00425 in 1,614,208 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R61C) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.0028 (1 hom., cov: 32)
  • Exomes 𝑓: 0.0044 (14 hom.)
• Consequence: SLC25A15 NM_014252.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:5 B:5
• Conservation: PhyloP100: 5.52
• Publications: 7 publications found

Genes affected

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]

SUGT1P3 (HGNC:):

TPTE2P5 (HGNC:42356): (TPTE2 pseudogene 5)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• PM1: In a repeat Solcar 1 (size 84) in uniprot entity ORNT1_HUMAN there are 7 pathogenic changes around while only 2 benign (78%) in NM_014252.4
• PP2: Missense variant in the gene, where a lot of missense mutations are associated with disease in ClinVar. The gene has 15 curated pathogenic missense variants (we use a threshold of 10). The gene has 4 curated benign missense variants. Gene score misZ: 0.10098 (below the threshold of 3.09). Trascript score misZ: 1.3225 (below the threshold of 3.09). GenCC associations: The gene is linked to ornithine translocase deficiency.
• BP4: Computational evidence support a benign effect (MetaRNN=0.018633276).
• BP6: Variant 13-40799183-G-A is Benign according to our data. Variant chr13-40799183-G-A is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 203939.
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.00283 (431/152316) while in subpopulation NFE AF = 0.0051 (347/68034). AF 95% confidence interval is 0.00466. There are 1 homozygotes in GnomAd4. There are 183 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAdExome4 at 14 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014252.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A15	NM_014252.4	MANE Select	c.182G>A	p.Arg61His	missense	Exon 3 of 7	NP_055067.1	Q9Y619
	TPTE2P5	NR_038258.1		n.2164C>T		non_coding_transcript_exon	Exon 8 of 8
	TPTE2P5	NR_038259.1		n.1993C>T		non_coding_transcript_exon	Exon 6 of 6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A15	ENST00000338625.9	TSL:1 MANE Select	c.182G>A	p.Arg61His	missense	Exon 3 of 7	ENSP00000342267.4	Q9Y619
	SLC25A15	ENST00000707033.1		c.182G>A	p.Arg61His	missense	Exon 3 of 7	ENSP00000516711.1	Q9Y619
	SLC25A15	ENST00000899653.1		c.182G>A	p.Arg61His	missense	Exon 3 of 7	ENSP00000569712.1

Frequencies

GnomAD3 genomes AF: 0.00283 AC: 431 AN: 152198 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.00106

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.00118

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000189

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00510

Gnomad OTH AF: 0.00287

GnomAD2 exomes AF: 0.00235 AC: 591 AN: 251426 AF XY: 0.00227

Gnomad AFR exome AF: 0.000984

Gnomad AMR exome AF: 0.000838

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.000462

Gnomad NFE exome AF: 0.00458

Gnomad OTH exome AF: 0.00244

GnomAD4 exome AF: 0.00440 AC: 6426 AN: 1461892 Hom.: 14 Cov.: 35 AF XY: 0.00427 AC XY: 3108 AN XY: 727248

African (AFR) AF: 0.000777 AC: 26 AN: 33480

American (AMR) AF: 0.00121 AC: 54 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.000115 AC: 3 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.0000232 AC: 2 AN: 86258

European-Finnish (FIN) AF: 0.000674 AC: 36 AN: 53420

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5768

European-Non Finnish (NFE) AF: 0.00545 AC: 6065 AN: 1112010

Other (OTH) AF: 0.00397 AC: 240 AN: 60396

GnomAD4 genome AF: 0.00283 AC: 431 AN: 152316 Hom.: 1 Cov.: 32 AF XY: 0.00246 AC XY: 183 AN XY: 74476

African (AFR) AF: 0.00106 AC: 44 AN: 41558

American (AMR) AF: 0.00118 AC: 18 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5194

South Asian (SAS) AF: 0.00 AC: 0 AN: 4828

European-Finnish (FIN) AF: 0.000189 AC: 2 AN: 10610

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.00510 AC: 347 AN: 68034

Other (OTH) AF: 0.00284 AC: 6 AN: 2112

Alfa AF: 0.00425 Hom.: 8

Bravo AF: 0.00289

TwinsUK AF: 0.00674 AC: 25

ALSPAC AF: 0.00285 AC: 11

ESP6500AA AF: 0.00159 AC: 7

ESP6500EA AF: 0.00535 AC: 46

ExAC AF: 0.00231 AC: 280

Asia WGS AF: 0.000289 AC: 1 AN: 3478

EpiCase AF: 0.00436

EpiControl AF: 0.00421

ClinVar

ClinVar submissions

Significance: Conflicting classifications of pathogenicity

Revision: criteria provided, conflicting classifications

Pathogenic	VUS	Benign	Condition
-	4	1	not provided (5)
-	1	2	Hyperornithinemia-hyperammonemia-homocitrullinuria syndrome (3)
-	-	1	Intellectual disability (1)
-	-	1	SLC25A15-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.26	T
BayesDel_noAF	Benign	-0.14
CADD	Uncertain	25
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.62	D
Eigen	Benign	-0.23
Eigen_PC	Benign	-0.22
FATHMM_MKL	Uncertain	0.88	D
LIST_S2	Uncertain	0.90	D
M_CAP	Uncertain	0.097	D
MetaRNN	Benign	0.019	T
MetaSVM	Benign	-0.49	T
MutationAssessor	Uncertain	2.6	M
PhyloP100		5.5
PrimateAI	Uncertain	0.58	T
PROVEAN	Uncertain	-3.2	D
REVEL	Uncertain	0.41
Sift	Benign	0.036	D
Sift4G	Uncertain	0.026	D
Polyphen		0.15	B
Vest4		0.66
MVP		0.84
MPC		0.14
ClinPred		0.070	T
GERP RS		2.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.073
gMVP		0.83
Mutation Taster		=87/13	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs34615430; hg19: chr13-41373319;