rs4463175

chr5-135603434-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000698884.1(ENSG00000250167):n.497-25803G>A variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.186 in 152,262 control chromosomes in the GnomAD database, including 2,724 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 0.19 (2724 hom., cov: 33)
• Consequence: ENST00000698884.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.36

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC25A48	NM_001349335.2	c.-849+23837G>A		intron_variant
SLC25A48	NM_001349345.2	c.-849+23837G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000698884.1	n.497-25803G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28222 AN: 152144 Hom.: 2715 Cov.: 33

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.186 AC: 28257 AN: 152262 Hom.: 2724 Cov.: 33 AF XY: 0.189 AC XY: 14073 AN XY: 74452

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.264

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.204

Alfa AF: 0.193 Hom.: 1367

Bravo AF: 0.182

Asia WGS AF: 0.297 AC: 1032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
Cadd	Benign	19
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4463175; hg19: chr5-134939124;