NM_207117.4:c.*419C>T

Variant names:

• chr14-100330064-C-T
• rs3736951
• NM_207117.4:c.*419C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_207117.4(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 NM_207117.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27
• Publications: 12 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_207117.4. 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
	SLC25A47	NM_207117.4	MANE Select	c.*419C>T		3_prime_UTR	Exon 6 of 6	NP_997000.2
	SLC25A47	NM_001350877.2		c.*419C>T		3_prime_UTR	Exon 6 of 6	NP_001337806.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A47	ENST00000361529.5	TSL:1 MANE Select	c.*419C>T		3_prime_UTR	Exon 6 of 6	ENSP00000354886.3
	SLC25A47	ENST00000557052.1	TSL:1	c.*419C>T		3_prime_UTR	Exon 6 of 6	ENSP00000451078.1

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

African (AFR) AF: 0.0997 AC: 158 AN: 1584

American (AMR) AF: 0.328 AC: 1146 AN: 3494

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 481 AN: 996

East Asian (EAS) AF: 0.216 AC: 422 AN: 1958

South Asian (SAS) AF: 0.676 AC: 3261 AN: 4824

European-Finnish (FIN) AF: 0.417 AC: 516 AN: 1238

Middle Eastern (MID) AF: 0.514 AC: 75 AN: 146

European-Non Finnish (NFE) AF: 0.500 AC: 12445 AN: 24878

Other (OTH) AF: 0.462 AC: 954 AN: 2066

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

African (AFR) AF: 0.103 AC: 4289 AN: 41546

American (AMR) AF: 0.343 AC: 5240 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.509 AC: 1766 AN: 3470

East Asian (EAS) AF: 0.227 AC: 1172 AN: 5170

South Asian (SAS) AF: 0.663 AC: 3197 AN: 4824

European-Finnish (FIN) AF: 0.414 AC: 4383 AN: 10590

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33944 AN: 67958

Other (OTH) AF: 0.400 AC: 846 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0090
DANN	Benign	0.40
PhyloP100		-2.3
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: rs3736951; hg19: chr14-100796401;