rs2344484

chr5-135540941-A-G

Variant summary

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

The ENST00000698884.1(ENSG00000250167):n.496+54172A>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 0.463 in 152,042 control chromosomes in the GnomAD database, including 19,267 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 0.46 (19267 hom., cov: 32)
• Consequence: ENST00000698884.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.568

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=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.765 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+54172A>G		intron_variant, non_coding_transcript_variant
SLC25A48	ENST00000698885.1	n.364+31185A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70241 AN: 151924 Hom.: 19218 Cov.: 32

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.463 AC: 70347 AN: 152042 Hom.: 19267 Cov.: 32 AF XY: 0.458 AC XY: 34011 AN XY: 74304

Gnomad4 AFR AF: 0.772

Gnomad4 AMR AF: 0.345

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.423

Alfa AF: 0.384 Hom.: 5643

Bravo AF: 0.477

Asia WGS AF: 0.472 AC: 1640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	11
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2344484; hg19: chr5-134876631;