chr14-100330064-C-T

Position:

• chr14-100330064-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000361529.5(SLC25A47):​c.*419C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 193,350 control chromosomes in the GnomAD database, including 17,649 homozygotes. 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 0.36 (12543 hom., cov: 33)
  • Exomes 𝑓: 0.47 (5106 hom.)
• Consequence: SLC25A47 ENST00000361529.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27

Genes affected

SLC25A47 (HGNC:20115): (solute carrier family 25 member 47) This gene encodes a member of a large family of mitochondrial transporters. The nuclear-encoded carrier protein is embedded in the inner mitochondrial membrane. This member of the family is thought to be an uncoupling protein that uncouples mitochondrial respiration from ATP synthesis by dissipating the transmembrane proton gradient. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC25A47	NM_207117.4	c.*419C>T		3_prime_UTR_variant	6/6	ENST00000361529.5	NP_997000.2
SLC25A47	NM_001350877.2	c.*419C>T		3_prime_UTR_variant	6/6		NP_001337806.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC25A47	ENST00000361529.5	c.*419C>T		3_prime_UTR_variant	6/6	1	NM_207117.4	ENSP00000354886	P1
SLC25A47	ENST00000557052.1	c.*419C>T		3_prime_UTR_variant	6/6	1		ENSP00000451078

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55341 AN: 152048 Hom.: 12532 Cov.: 33

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.399

GnomAD4 exome AF: 0.472 AC: 19458 AN: 41184 Hom.: 5106 Cov.: 0 AF XY: 0.485 AC XY: 10442 AN XY: 21518

Gnomad4 AFR exome AF: 0.0997

Gnomad4 AMR exome AF: 0.328

Gnomad4 ASJ exome AF: 0.483

Gnomad4 EAS exome AF: 0.216

Gnomad4 SAS exome AF: 0.676

Gnomad4 FIN exome AF: 0.417

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.462

GnomAD4 genome AF: 0.364 AC: 55358 AN: 152166 Hom.: 12543 Cov.: 33 AF XY: 0.364 AC XY: 27054 AN XY: 74388

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.400

Alfa AF: 0.334 Hom.: 1275

Bravo AF: 0.341

Asia WGS AF: 0.412 AC: 1436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0090
DANN	Benign	0.40

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: rs3736951; hg19: chr14-100796401;