5-135532951-C-G

Position:

• chr5-135532951-C-G

Variant summary

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

The ENST00000698884.1(ENSG00000250167):​n.496+46182C>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0693 in 151,952 control chromosomes in the GnomAD database, including 554 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 0.069 (554 hom., cov: 32)
• Consequence: ENST00000698884.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460

Genes affected

(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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000698884.1	n.496+46182C>G		intron_variant, non_coding_transcript_variant
SLC25A48	ENST00000698885.1	n.364+23195C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0694 AC: 10535 AN: 151834 Hom.: 555 Cov.: 32

Gnomad AFR AF: 0.0183

Gnomad AMI AF: 0.0484

Gnomad AMR AF: 0.0531

Gnomad ASJ AF: 0.0635

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.0374

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0946

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.0693 AC: 10527 AN: 151952 Hom.: 554 Cov.: 32 AF XY: 0.0693 AC XY: 5147 AN XY: 74266

Gnomad4 AFR AF: 0.0182

Gnomad4 AMR AF: 0.0530

Gnomad4 ASJ AF: 0.0635

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.0374

Gnomad4 NFE AF: 0.0947

Gnomad4 OTH AF: 0.0681

Alfa AF: 0.0753 Hom.: 71

Bravo AF: 0.0660

Asia WGS AF: 0.132 AC: 459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.2
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2344485; hg19: chr5-134868641;