19-19111261-C-T

Position:

• chr19-19111261-C-T

Variant summary

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

The NM_178526.5(SLC25A42):​c.*385C>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 0.786 in 242,172 control chromosomes in the GnomAD database, including 75,582 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 0.77 (45642 hom., cov: 33)
  • Exomes 𝑓: 0.81 (29940 hom.)
• Consequence: SLC25A42 NM_178526.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.808

Genes affected

SLC25A42 (HGNC:28380): (solute carrier family 25 member 42) This gene encodes a solute carrier family 25 protein. Solute carrier family 25 proteins are localized to mitochondria and play critical roles in the transport of molecules across the inner mitochondrial membrane. The encoded protein is a mitochondrial transporter for coenzyme A (CoA) and adenosine 3',5'-diphosphate. [provided by RefSeq, Feb 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC25A42	NM_178526.5	c.*385C>T		3_prime_UTR_variant	8/8	ENST00000318596.8
SLC25A42	NM_001321544.2	c.*385C>T		3_prime_UTR_variant	8/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC25A42	ENST00000318596.8	c.*385C>T		3_prime_UTR_variant	8/8	1	NM_178526.5	P1

Frequencies

GnomAD3 genomes AF: 0.770 AC: 117042 AN: 152046 Hom.: 45624 Cov.: 33

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.935

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.828

Gnomad EAS AF: 0.906

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.801

GnomAD4 exome AF: 0.813 AC: 73184 AN: 90008 Hom.: 29940 Cov.: 0 AF XY: 0.814 AC XY: 39096 AN XY: 48028

Gnomad4 AFR exome AF: 0.641

Gnomad4 AMR exome AF: 0.835

Gnomad4 ASJ exome AF: 0.842

Gnomad4 EAS exome AF: 0.910

Gnomad4 SAS exome AF: 0.809

Gnomad4 FIN exome AF: 0.777

Gnomad4 NFE exome AF: 0.815

Gnomad4 OTH exome AF: 0.811

GnomAD4 genome AF: 0.770 AC: 117103 AN: 152164 Hom.: 45642 Cov.: 33 AF XY: 0.770 AC XY: 57274 AN XY: 74400

Gnomad4 AFR AF: 0.643

Gnomad4 AMR AF: 0.818

Gnomad4 ASJ AF: 0.828

Gnomad4 EAS AF: 0.907

Gnomad4 SAS AF: 0.811

Gnomad4 FIN AF: 0.765

Gnomad4 NFE AF: 0.817

Gnomad4 OTH AF: 0.799

Alfa AF: 0.798 Hom.: 19184

Bravo AF: 0.772

Asia WGS AF: 0.831 AC: 2894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.16
DANN	Benign	0.77

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: rs10417974; hg19: chr19-19222070; COSMIC: COSV59381855; COSMIC: COSV59381855;