rs6511018

Variant names:

• chr19-19075896-G-A
• rs6511018
• NM_178526.5:c.-35+11781G>A

Your query was ambiguous. Multiple possible variants found:

• chr19-19075896-G-A
• chr19-19075896-G-C
• chr19-19075896-G-T

Variant summary

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

The NM_178526.5(SLC25A42):​c.-35+11781G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.77 in 152,010 control chromosomes in the GnomAD database, including 45,657 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 (45657 hom., cov: 31)
• Consequence: SLC25A42 NM_178526.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0870
• Publications: 10 publications found

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]

SLC25A42 Gene-Disease associations (from GenCC):

• metabolic crises, recurrent, with variable encephalomyopathic features and neurologic regression

  Inheritance: AR Classification: STRONG, MODERATE Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae), PanelApp Australia

ENSG00000296554 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178526.5. 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
	SLC25A42	NM_178526.5	MANE Select	c.-35+11781G>A		intron	N/A	NP_848621.2	Q86VD7
	SLC25A42	NM_001321544.2		c.-35+11850G>A		intron	N/A	NP_001308473.1	Q86VD7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A42	ENST00000318596.8	TSL:1 MANE Select	c.-35+11781G>A		intron	N/A	ENSP00000326693.6	Q86VD7
	SLC25A42	ENST00000857041.1		c.-35+11850G>A		intron	N/A	ENSP00000527100.1
	SLC25A42	ENST00000857042.1		c.-132-10790G>A		intron	N/A	ENSP00000527101.1

Frequencies

GnomAD3 genomes AF: 0.770 AC: 117017 AN: 151890 Hom.: 45638 Cov.: 31

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.830

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.770 AC: 117080 AN: 152010 Hom.: 45657 Cov.: 31 AF XY: 0.770 AC XY: 57224 AN XY: 74290

African (AFR) AF: 0.643 AC: 26624 AN: 41394

American (AMR) AF: 0.819 AC: 12505 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.830 AC: 2880 AN: 3470

East Asian (EAS) AF: 0.890 AC: 4604 AN: 5172

South Asian (SAS) AF: 0.812 AC: 3919 AN: 4826

European-Finnish (FIN) AF: 0.765 AC: 8079 AN: 10566

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.819 AC: 55703 AN: 67990

Other (OTH) AF: 0.799 AC: 1688 AN: 2112

Alfa AF: 0.813 Hom.: 66222

Bravo AF: 0.772

Asia WGS AF: 0.827 AC: 2877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.70
PhyloP100		0.087
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: rs6511018; hg19: chr19-19186705;