chr5-135532951-C-G

Variant names:

• chr5-135532951-C-G
• rs2344485
• ENST00000698884.1:n.496+46182C>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+46182C>G variant causes a intron 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: ENSG00000250167 ENST00000698884.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460
• Publications: 4 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=-0.86).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000250167	ENST00000698884.1	n.496+46182C>G		intron_variant	Intron 3 of 5
SLC25A48	ENST00000698885.1	n.364+23195C>G		intron_variant	Intron 2 of 3

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

African (AFR) AF: 0.0182 AC: 756 AN: 41456

American (AMR) AF: 0.0530 AC: 808 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.0635 AC: 220 AN: 3464

East Asian (EAS) AF: 0.145 AC: 748 AN: 5168

South Asian (SAS) AF: 0.197 AC: 947 AN: 4806

European-Finnish (FIN) AF: 0.0374 AC: 394 AN: 10532

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0947 AC: 6433 AN: 67960

Other (OTH) AF: 0.0681 AC: 144 AN: 2114

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
PhyloP100		0.046

Splicing

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

Other links and lift over

dbSNP: rs2344485; hg19: chr5-134868641;