rs2344484

Variant names:

• chr5-135540941-A-G
• rs2344484
• ENST00000698884.1:n.496+54172A>G

Variant summary

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

The ENST00000698884.1(ENSG00000250167):​n.496+54172A>G variant causes a intron 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: ENSG00000250167 ENST00000698884.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.568
• Publications: 6 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=-0.75).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000250167	ENST00000698884.1	n.496+54172A>G		intron_variant	Intron 3 of 5
SLC25A48	ENST00000698885.1	n.364+31185A>G		intron_variant	Intron 2 of 3

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

African (AFR) AF: 0.772 AC: 32030 AN: 41476

American (AMR) AF: 0.345 AC: 5279 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1206 AN: 3470

East Asian (EAS) AF: 0.359 AC: 1848 AN: 5152

South Asian (SAS) AF: 0.516 AC: 2479 AN: 4800

European-Finnish (FIN) AF: 0.263 AC: 2782 AN: 10570

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.346 AC: 23555 AN: 67980

Other (OTH) AF: 0.423 AC: 891 AN: 2104

Alfa AF: 0.383 Hom.: 6188

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
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs2344484; hg19: chr5-134876631;