rs5977248

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001282195.2(SLC25A14):​c.855+1837G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 110,283 control chromosomes in the GnomAD database, including 6,535 homozygotes. There are 12,509 hemizygotes in GnomAD. 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 0.40 ( 6535 hom., 12509 hem., cov: 22)

Consequence

SLC25A14
NM_001282195.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.202
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SLC25A14NM_001282195.2 linkuse as main transcriptc.855+1837G>T intron_variant ENST00000545805.6 NP_001269124.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLC25A14ENST00000545805.6 linkuse as main transcriptc.855+1837G>T intron_variant 5 NM_001282195.2 ENSP00000444642 O95258-1

Frequencies

GnomAD3 genomes
AF:
0.402
AC:
44258
AN:
110226
Hom.:
6539
Cov.:
22
AF XY:
0.384
AC XY:
12495
AN XY:
32554
show subpopulations
Gnomad AFR
AF:
0.359
Gnomad AMI
AF:
0.342
Gnomad AMR
AF:
0.369
Gnomad ASJ
AF:
0.406
Gnomad EAS
AF:
0.377
Gnomad SAS
AF:
0.411
Gnomad FIN
AF:
0.321
Gnomad MID
AF:
0.418
Gnomad NFE
AF:
0.443
Gnomad OTH
AF:
0.392
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.401
AC:
44246
AN:
110283
Hom.:
6535
Cov.:
22
AF XY:
0.383
AC XY:
12509
AN XY:
32621
show subpopulations
Gnomad4 AFR
AF:
0.359
Gnomad4 AMR
AF:
0.368
Gnomad4 ASJ
AF:
0.406
Gnomad4 EAS
AF:
0.378
Gnomad4 SAS
AF:
0.411
Gnomad4 FIN
AF:
0.321
Gnomad4 NFE
AF:
0.443
Gnomad4 OTH
AF:
0.387
Alfa
AF:
0.439
Hom.:
41201
Bravo
AF:
0.405

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.81
DANN
Benign
0.30

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs5977248; hg19: chrX-129501487; API