rs10515473

Variant names:

• chr5-135598397-C-A
• rs10515473
• NM_001349335.2:c.-849+18800C>A

Your query was ambiguous. Multiple possible variants found:

• chr5-135598397-C-A
• chr5-135598397-C-T

Variant summary

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

The NM_001349335.2(SLC25A48):​c.-849+18800C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 152,074 control chromosomes in the GnomAD database, including 6,168 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 (6168 hom., cov: 33)
• Consequence: SLC25A48 NM_001349335.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.558
• Publications: 3 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC25A48	NM_001349335.2	c.-849+18800C>A		intron_variant	Intron 1 of 10		NP_001336264.1
SLC25A48	NM_001349345.2	c.-849+18800C>A		intron_variant	Intron 1 of 9		NP_001336274.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC25A48	ENST00000646290.1	c.-849+18800C>A		intron_variant	Intron 1 of 10			ENSP00000493514.1
ENSG00000250167	ENST00000509372.1	n.75-2653C>A		intron_variant	Intron 1 of 3	3
ENSG00000250167	ENST00000514446.1	n.413+18800C>A		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42052 AN: 151956 Hom.: 6148 Cov.: 33

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.265

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.277 AC: 42122 AN: 152074 Hom.: 6168 Cov.: 33 AF XY: 0.271 AC XY: 20161 AN XY: 74336

African (AFR) AF: 0.349 AC: 14480 AN: 41468

American (AMR) AF: 0.183 AC: 2793 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1032 AN: 3470

East Asian (EAS) AF: 0.104 AC: 535 AN: 5164

South Asian (SAS) AF: 0.224 AC: 1079 AN: 4810

European-Finnish (FIN) AF: 0.297 AC: 3141 AN: 10572

Middle Eastern (MID) AF: 0.278 AC: 80 AN: 288

European-Non Finnish (NFE) AF: 0.268 AC: 18249 AN: 68000

Other (OTH) AF: 0.260 AC: 549 AN: 2114

Alfa AF: 0.259 Hom.: 8901

Bravo AF: 0.269

Asia WGS AF: 0.168 AC: 587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.40
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs10515473; hg19: chr5-134934087;