NM_001034172.4:c.307G>A

Variant names:

• chr18-31760355-C-T
• NM_001034172.4:c.307G>A

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001034172.4(SLC25A52):​c.307G>A​(p.Glu103Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: SLC25A52 NM_001034172.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.41
• Publications: 0 publications found

Genes affected

SLC25A52 (HGNC:23324): (solute carrier family 25 member 52) This gene is similar to the mitochondrial carrier triple repeat 1 gene on chromosome 9. The gene is intronless and may be an evolving pseudogene; however, it is transcribed and it contains a full-length coding region so it is currently classified as a protein-coding locus. [provided by RefSeq, Jul 2008]

ENSG00000293306 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001034172.4. 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
	SLC25A52	NM_001034172.4	MANE Select	c.307G>A	p.Glu103Lys	missense	Exon 1 of 1	NP_001029344.4	Q3SY17

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A52	ENST00000269205.7	TSL:6 MANE Select	c.307G>A	p.Glu103Lys	missense	Exon 1 of 1	ENSP00000372612.4	Q3SY17
	SLC25A52	ENST00000672005.1		c.337G>A	p.Glu113Lys	missense	Exon 1 of 1	ENSP00000500333.1	I3L0B8
	ENSG00000293306	ENST00000723809.1		n.1000-1784C>T		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.24
BayesDel_addAF	Uncertain	0.063	T
BayesDel_noAF	Benign	-0.15
CADD	Benign	19
DANN	Uncertain	1.0
DEOGEN2	Benign	0.26	T
Eigen	Benign	0.084
Eigen_PC	Benign	-0.063
FATHMM_MKL	Benign	0.30	N
LIST_S2	Benign	0.76	T
M_CAP	Benign	0.0043	T
MetaRNN	Uncertain	0.44	T
MetaSVM	Uncertain	0.29	D
PhyloP100		1.4
PrimateAI	Uncertain	0.58	T
PROVEAN	Benign	-2.1	N
REVEL	Uncertain	0.59
Sift	Uncertain	0.014	D
Sift4G	Benign	0.063	T
Vest4		0.38
MVP		0.73
MPC		0.97
ClinPred		0.96	D
GERP RS		1.0
gMVP		0.53
Mutation Taster		=94/6	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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

hg19: chr18-29340318;