19-19076766-C-T

Position:

• chr19-19076766-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.-35+12651C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.78 in 152,130 control chromosomes in the GnomAD database, including 46,781 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 0.78 (46781 hom., cov: 33)
• Consequence: SLC25A42 NM_178526.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.967

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC25A42	NM_178526.5	c.-35+12651C>T		intron_variant		ENST00000318596.8	NP_848621.2
SLC25A42	NM_001321544.2	c.-35+12720C>T		intron_variant			NP_001308473.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC25A42	ENST00000318596.8	c.-35+12651C>T		intron_variant		1	NM_178526.5	ENSP00000326693	P1
SLC25A42	ENST00000597661.5	n.29+12720C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.780 AC: 118605 AN: 152010 Hom.: 46756 Cov.: 33

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.847

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.824

Gnomad OTH AF: 0.812

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.780 AC: 118685 AN: 152130 Hom.: 46781 Cov.: 33 AF XY: 0.780 AC XY: 58014 AN XY: 74372

Gnomad4 AFR AF: 0.665

Gnomad4 AMR AF: 0.830

Gnomad4 ASJ AF: 0.847

Gnomad4 EAS AF: 0.890

Gnomad4 SAS AF: 0.814

Gnomad4 FIN AF: 0.765

Gnomad4 NFE AF: 0.824

Gnomad4 OTH AF: 0.809

Alfa AF: 0.745 Hom.: 3875

Bravo AF: 0.783

Asia WGS AF: 0.830 AC: 2888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.4
DANN	Benign	0.41

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: rs12985799; hg19: chr19-19187575;