X-119433739-T-C

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_145305.3(SLC25A43):​c.691-18270T>C 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: 𝑓 0.77 (22936 hom., 24984 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: SLC25A43 NM_145305.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.655
• Publications: 5 publications found

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

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.766 AC: 84576 AN: 110381 Hom.: 22939 Cov.: 23

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.751

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.766 AC: 84610 AN: 110435 Hom.: 22936 Cov.: 23 AF XY: 0.765 AC XY: 24984 AN XY: 32675

African (AFR) AF: 0.818 AC: 24858 AN: 30380

American (AMR) AF: 0.721 AC: 7415 AN: 10279

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2047 AN: 2630

East Asian (EAS) AF: 0.637 AC: 2222 AN: 3490

South Asian (SAS) AF: 0.792 AC: 2068 AN: 2610

European-Finnish (FIN) AF: 0.748 AC: 4352 AN: 5817

Middle Eastern (MID) AF: 0.743 AC: 159 AN: 214

European-Non Finnish (NFE) AF: 0.754 AC: 39872 AN: 52867

Other (OTH) AF: 0.753 AC: 1112 AN: 1477

Alfa AF: 0.759 Hom.: 127642

Bravo AF: 0.764

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.21
DANN	Benign	0.54
PhyloP100		-0.66
Mutation Taster		=100/0	polymorphism (auto)

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: rs5910578; hg19: chrX-118567702;