chr5-135864020-A-C

Position:

• chr5-135864020-A-C

Variant summary

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

The NM_001349336.2(SLC25A48):​c.422-7441A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 152,090 control chromosomes in the GnomAD database, including 48,586 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 0.80 (48586 hom., cov: 32)
• Consequence: SLC25A48 NM_001349336.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.917

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC25A48	NM_001349336.2	c.422-7441A>C		intron_variant		ENST00000681962.1	NP_001336265.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC25A48	ENST00000681962.1	c.422-7441A>C		intron_variant			NM_001349336.2	ENSP00000506858	P1

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121229 AN: 151972 Hom.: 48545 Cov.: 32

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.824

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.798 AC: 121328 AN: 152090 Hom.: 48586 Cov.: 32 AF XY: 0.794 AC XY: 59033 AN XY: 74356

Gnomad4 AFR AF: 0.744

Gnomad4 AMR AF: 0.790

Gnomad4 ASJ AF: 0.824

Gnomad4 EAS AF: 0.699

Gnomad4 SAS AF: 0.813

Gnomad4 FIN AF: 0.769

Gnomad4 NFE AF: 0.839

Gnomad4 OTH AF: 0.823

Alfa AF: 0.837 Hom.: 70240

Bravo AF: 0.795

Asia WGS AF: 0.770 AC: 2680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.31

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: rs4246802; hg19: chr5-135199709; COSMIC: COSV50848421;