5-135825366-A-C

Variant names:

• chr5-135825366-A-C
• rs17169180
• NM_001349335.2:c.-117+12440A>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.-117+12440A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,194 control chromosomes in the GnomAD database, including 2,854 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 0.18 (2854 hom., cov: 32)
• Consequence: SLC25A48 NM_001349335.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.813
• Publications: 5 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]

ENSG00000250378 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC25A48	NM_001349335.2	c.-117+12440A>C		intron_variant	Intron 4 of 10		NP_001336264.1
SLC25A48	NM_001349345.2	c.-117+12440A>C		intron_variant	Intron 4 of 9		NP_001336274.1
LOC107986453	NR_171171.1	n.579-359A>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC25A48	ENST00000646290.1	c.-117+12440A>C		intron_variant	Intron 4 of 10			ENSP00000493514.1
ENSG00000250378	ENST00000506592.1	n.261-1100A>C		intron_variant	Intron 1 of 1	3
ENSG00000250378	ENST00000637197.2	n.787-359A>C		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27913 AN: 152076 Hom.: 2847 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.184 AC: 27944 AN: 152194 Hom.: 2854 Cov.: 32 AF XY: 0.188 AC XY: 13972 AN XY: 74414

African (AFR) AF: 0.201 AC: 8346 AN: 41532

American (AMR) AF: 0.172 AC: 2627 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 677 AN: 3472

East Asian (EAS) AF: 0.436 AC: 2247 AN: 5152

South Asian (SAS) AF: 0.277 AC: 1338 AN: 4824

European-Finnish (FIN) AF: 0.184 AC: 1954 AN: 10606

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10098 AN: 68004

Other (OTH) AF: 0.205 AC: 433 AN: 2110

Alfa AF: 0.159 Hom.: 3920

Bravo AF: 0.183

Asia WGS AF: 0.351 AC: 1217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.065
DANN	Benign	0.54
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs17169180; hg19: chr5-135161055;