5-135545302-T-C

Position:

• chr5-135545302-T-C

Variant summary

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

The ENST00000698884.1(ENSG00000250167):​n.496+58533T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 152,068 control chromosomes in the GnomAD database, including 24,746 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 0.53 (24746 hom., cov: 32)
• Consequence: ENSG00000250167 ENST00000698884.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.677

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000250167	ENST00000698884.1	n.496+58533T>C		intron_variant
SLC25A48	ENST00000698885.1	n.364+35546T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80666 AN: 151950 Hom.: 24742 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.531 AC: 80684 AN: 152068 Hom.: 24746 Cov.: 32 AF XY: 0.535 AC XY: 39791 AN XY: 74342

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.644

Gnomad4 EAS AF: 0.641

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.734

Gnomad4 NFE AF: 0.655

Gnomad4 OTH AF: 0.572

Alfa AF: 0.575 Hom.: 6055

Bravo AF: 0.515

Asia WGS AF: 0.535 AC: 1861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.5
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs245128; hg19: chr5-134880992;