X-119433739-T-G

Variant names:

• chrX-119433739-T-G
• rs5910578
• NM_145305.3:c.691-18270T>G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_145305.3(SLC25A43):​c.691-18270T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 23)
• Consequence: SLC25A43 NM_145305.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.655

Genes affected

SLC25A43 (HGNC:30557): (solute carrier family 25 member 43) This gene encodes a member of the mitochondrial carrier family of proteins.[provided by RefSeq, Dec 2009]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC25A43	NM_145305.3	c.691-18270T>G		intron_variant	Intron 3 of 4	ENST00000217909.8	NP_660348.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC25A43	ENST00000217909.8	c.691-18270T>G		intron_variant	Intron 3 of 4	1	NM_145305.3	ENSP00000217909.7
SLC25A43	ENST00000484058.1	n.147-18270T>G		intron_variant	Intron 1 of 2	2
SLC25A43	ENST00000488158.5	n.887+7385T>G		intron_variant	Intron 4 of 5	2
SLC25A43	ENST00000493093.5	n.444-18270T>G		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes Cov.: 23

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

GnomAD4 genome Cov.: 23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.55

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: rs5910578; hg19: chrX-118567702;