chrX-130364862-T-C

Variant names:

• chrX-130364862-T-C
• rs2235800
• NM_001282195.2:c.719+110T>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001282195.2(SLC25A14):​c.719+110T>C 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: 22)
  • Exomes 𝑓: 9.9e-7 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: SLC25A14 NM_001282195.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632
• Publications: 4 publications found

Genes affected

SLC25A14 (HGNC:10984): (solute carrier family 25 member 14) Mitochondrial uncoupling proteins (UCP) are members of the larger family of mitochondrial anion carrier proteins (MACP). Uncoupling proteins separate oxidative phosphorylation from ATP synthesis with energy dissipated as heat, also referred to as the mitochondrial proton leak. Uncoupling proteins facilitate the transfer of anions from the inner to the outer mitochondrial membrane and the return transfer of protons from the outer to the inner mitochondrial membrane. They also reduce the mitochondrial membrane potential in mammalian cells. This gene is widely expressed in many tissues with the greatest abundance in brain and testis. Alternative splicing results in multiple transcript variants. A pseudogene of this gene has been defined on chromosome 4. [provided by RefSeq, Aug 2013]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001282195.2. 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
	SLC25A14	NM_001282195.2	MANE Select	c.719+110T>C		intron	N/A	NP_001269124.1	O95258-1
	SLC25A14	NM_001282197.2		c.803+110T>C		intron	N/A	NP_001269126.1	O95258-3
	SLC25A14	NM_001282196.2		c.710+110T>C		intron	N/A	NP_001269125.1	O95258-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A14	ENST00000545805.6	TSL:5 MANE Select	c.719+110T>C		intron	N/A	ENSP00000444642.2	O95258-1
	SLC25A14	ENST00000339231.3	TSL:1	c.803+110T>C		intron	N/A	ENSP00000342797.3	O95258-3
	SLC25A14	ENST00000218197.9	TSL:1	c.719+110T>C		intron	N/A	ENSP00000218197.5	O95258-1

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 9.94e-7 AC: 1 AN: 1006246 Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0 AN XY: 306824

African (AFR) AF: 0.00 AC: 0 AN: 23828

American (AMR) AF: 0.00 AC: 0 AN: 26820

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16835

East Asian (EAS) AF: 0.00 AC: 0 AN: 25133

South Asian (SAS) AF: 0.00 AC: 0 AN: 49100

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 28326

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3720

European-Non Finnish (NFE) AF: 0.00000126 AC: 1 AN: 791086

Other (OTH) AF: 0.00 AC: 0 AN: 41398

GnomAD4 genome Cov.: 22

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.67
DANN	Benign	0.74
PhyloP100		-0.63

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2235800;

hg19: chrX-129498836;