13-45408979-G-C

Variant names:

• chr13-45408979-G-C
• rs1001035017
• NM_001010875.4:c.160C>G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001010875.4(SLC25A30):​c.160C>G​(p.His54Asp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SLC25A30 NM_001010875.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 9.45

Genes affected

SLC25A30 (HGNC:27371): (solute carrier family 25 member 30) Although the outer mitochondrial membrane is permeable to many small metabolites, transport of solutes across the inner mitochondrial membrane is achieved by members of the mitochondrial carrier protein family, such as SLC25A30 (Haguenauer et al., 2005 [PubMed 15809292]).[supplied by OMIM, Mar 2008]

TPT1-AS1 (HGNC:43686): (TPT1 antisense RNA 1) Biomarker of malignant astrocytoma. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC25A30	NM_001010875.4	c.160C>G	p.His54Asp	missense_variant	Exon 3 of 10	ENST00000519676.6	NP_001010875.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC25A30	ENST00000519676.6	c.160C>G	p.His54Asp	missense_variant	Exon 3 of 10	1	NM_001010875.4	ENSP00000429168.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Pathogenic	0.32	D
BayesDel_noAF	Pathogenic	0.22
CADD	Benign	22
DANN	Benign	0.95
DEOGEN2	Benign	0.34	T;.;T
Eigen	Benign	0.048
Eigen_PC	Benign	0.20
FATHMM_MKL	Pathogenic	1.0	D
LIST_S2	Uncertain	0.93	D;T;T
M_CAP	Benign	0.041	D
MetaRNN	Uncertain	0.62	D;D;D
MetaSVM	Benign	-0.76	T
MutationAssessor	Benign	0.27	N;.;.
PrimateAI	Uncertain	0.74	T
PROVEAN	Uncertain	-3.9	D;D;D
REVEL	Uncertain	0.48
Sift	Benign	0.78	T;T;T
Sift4G	Benign	1.0	T;T;.
Polyphen		0.38	B;.;.
Vest4		0.90
MutPred		0.61		Loss of MoRF binding (P = 0.0664);.;.;
MVP		0.85
MPC		0.48
ClinPred		0.79	D
GERP RS		6.1
Varity_R		0.36
gMVP		0.96

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

Publications

LitVar

Other links and lift over

dbSNP: rs1001035017; hg19: chr13-45983114;