5-135828929-A-C

Variant names:

• chr5-135828929-A-C
• rs13178541
• NM_001349335.2:c.-116-13487A>C

Variant summary

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

The NM_001349335.2(SLC25A48):​c.-116-13487A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 152,094 control chromosomes in the GnomAD database, including 39,527 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 0.71 (39527 hom., cov: 33)
• Consequence: SLC25A48 NM_001349335.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.691
• Publications: 6 publications found

Genes affected

SLC25A48 (HGNC:30451): (solute carrier family 25 member 48) Predicted to enable acyl carnitine transmembrane transporter activity. Predicted to be involved in acyl carnitine transport and amino acid transport. Predicted to be located in mitochondrial inner membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001349335.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A48	NM_001349335.2		c.-116-13487A>C		intron	N/A	NP_001336264.1
	SLC25A48	NM_001349345.2		c.-116-13487A>C		intron	N/A	NP_001336274.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A48	ENST00000646290.1		c.-116-13487A>C		intron	N/A	ENSP00000493514.1

Frequencies

GnomAD3 genomes AF: 0.712 AC: 108136 AN: 151976 Hom.: 39503 Cov.: 33

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.711 AC: 108206 AN: 152094 Hom.: 39527 Cov.: 33 AF XY: 0.711 AC XY: 52841 AN XY: 74352

African (AFR) AF: 0.542 AC: 22463 AN: 41472

American (AMR) AF: 0.678 AC: 10354 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2691 AN: 3470

East Asian (EAS) AF: 0.704 AC: 3624 AN: 5150

South Asian (SAS) AF: 0.732 AC: 3528 AN: 4820

European-Finnish (FIN) AF: 0.779 AC: 8248 AN: 10584

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.804 AC: 54665 AN: 68002

Other (OTH) AF: 0.748 AC: 1579 AN: 2110

Alfa AF: 0.635 Hom.: 4592

Bravo AF: 0.692

Asia WGS AF: 0.729 AC: 2537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.2
DANN	Benign	0.66
PhyloP100		0.69

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs13178541; hg19: chr5-135164618; COSMIC: COSV72644585; COSMIC: COSV72644585;