chr5-135603434-G-A

Variant names:

• chr5-135603434-G-A
• rs4463175
• NM_001349335.2:c.-849+23837G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001349335.2(SLC25A48):​c.-849+23837G>A variant causes a intron 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: SLC25A48 NM_001349335.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.36
• Publications: 4 publications found

Genes affected

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]

ENSG00000250167 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001349335.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A48	NM_001349335.2		c.-849+23837G>A		intron	N/A	NP_001336264.1
	SLC25A48	NM_001349345.2		c.-849+23837G>A		intron	N/A	NP_001336274.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A48	ENST00000646290.1		c.-849+23837G>A		intron	N/A	ENSP00000493514.1
	ENSG00000250167	ENST00000509372.1	TSL:3	n.228+2231G>A		intron	N/A
	ENSG00000250167	ENST00000514446.1	TSL:3	n.413+23837G>A		intron	N/A

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

African (AFR) AF: 0.165 AC: 6840 AN: 41560

American (AMR) AF: 0.169 AC: 2581 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 756 AN: 3472

East Asian (EAS) AF: 0.305 AC: 1578 AN: 5176

South Asian (SAS) AF: 0.264 AC: 1276 AN: 4828

European-Finnish (FIN) AF: 0.173 AC: 1830 AN: 10600

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12787 AN: 68002

Other (OTH) AF: 0.204 AC: 430 AN: 2110

Alfa AF: 0.192 Hom.: 1493

Bravo AF: 0.182

Asia WGS AF: 0.297 AC: 1032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	19
DANN	Benign	0.61
PhyloP100		4.4

Splicing

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

Other links and lift over

dbSNP: rs4463175; hg19: chr5-134939124;