ENST00000509372.1:n.74+1493C>T

Variant names:

• chr5-135561143-C-T
• rs10038760
• ENST00000509372.1:n.74+1493C>T

Variant summary

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

The ENST00000509372.1(ENSG00000250167):​n.74+1493C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,154 control chromosomes in the GnomAD database, including 1,542 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 0.14 (1542 hom., cov: 33)
• Consequence: ENSG00000250167 ENST00000509372.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.24
• Publications: 3 publications found

Genes affected

ENSG00000250167 (HGNC:):

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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000509372.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000250167	ENST00000509372.1	TSL:3	n.74+1493C>T		intron	N/A
	ENSG00000250167	ENST00000698884.1		n.497-68094C>T		intron	N/A
	SLC25A48	ENST00000698885.1		n.364+51387C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20835 AN: 152036 Hom.: 1541 Cov.: 33

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.137 AC: 20844 AN: 152154 Hom.: 1542 Cov.: 33 AF XY: 0.140 AC XY: 10389 AN XY: 74352

African (AFR) AF: 0.115 AC: 4761 AN: 41508

American (AMR) AF: 0.146 AC: 2235 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 501 AN: 3472

East Asian (EAS) AF: 0.302 AC: 1557 AN: 5154

South Asian (SAS) AF: 0.228 AC: 1099 AN: 4820

European-Finnish (FIN) AF: 0.100 AC: 1060 AN: 10580

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9146 AN: 68006

Other (OTH) AF: 0.154 AC: 325 AN: 2112

Alfa AF: 0.138 Hom.: 5867

Bravo AF: 0.139

Asia WGS AF: 0.276 AC: 956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.36
DANN	Benign	0.73
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs10038760; hg19: chr5-134896833;