NM_001349335.2:c.-708-1497G>C

Variant names:

• chr5-135633272-G-C
• rs31263
• NM_001349335.2:c.-708-1497G>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.-708-1497G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 151,972 control chromosomes in the GnomAD database, including 6,634 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 0.28 (6634 hom., cov: 31)
• Consequence: SLC25A48 NM_001349335.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 2 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]

ENSG00000250167 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.575 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.-708-1497G>C		intron	N/A	NP_001336264.1
	SLC25A48	NM_001349345.2		c.-708-1497G>C		intron	N/A	NP_001336274.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A48	ENST00000646290.1		c.-708-1497G>C		intron	N/A	ENSP00000493514.1
	ENSG00000250167	ENST00000509372.1	TSL:3	n.369-1497G>C		intron	N/A
	ENSG00000250167	ENST00000514446.1	TSL:3	n.551-1497G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43121 AN: 151854 Hom.: 6619 Cov.: 31

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.284 AC: 43164 AN: 151972 Hom.: 6634 Cov.: 31 AF XY: 0.290 AC XY: 21514 AN XY: 74266

African (AFR) AF: 0.211 AC: 8737 AN: 41476

American (AMR) AF: 0.343 AC: 5240 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 692 AN: 3468

East Asian (EAS) AF: 0.593 AC: 3048 AN: 5140

South Asian (SAS) AF: 0.375 AC: 1804 AN: 4808

European-Finnish (FIN) AF: 0.341 AC: 3591 AN: 10530

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19283 AN: 67972

Other (OTH) AF: 0.286 AC: 603 AN: 2110

Alfa AF: 0.278 Hom.: 719

Bravo AF: 0.284

Asia WGS AF: 0.461 AC: 1599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.6
DANN	Benign	0.73
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs31263; hg19: chr5-134968962;