rs5910578

chrX-119433739-T-AchrX-119433739-T-CchrX-119433739-T-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_145305.3(SLC25A43):c.691-18270T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC25A43	NM_145305.3	c.691-18270T>A		intron_variant		ENST00000217909.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC25A43	ENST00000217909.8	c.691-18270T>A		intron_variant		1	NM_145305.3	P1
SLC25A43	ENST00000484058.1	n.147-18270T>A		intron_variant, non_coding_transcript_variant		2
SLC25A43	ENST00000488158.5	n.887+7385T>A		intron_variant, non_coding_transcript_variant		2
SLC25A43	ENST00000493093.5	n.444-18270T>A		intron_variant, non_coding_transcript_variant		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	-0.97
Cadd	Benign	0.19
Dann	Benign	0.51

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;