rs6596238

Variant names:

• chr5-135528766-G-A
• rs6596238
• ENST00000698884.1:n.496+41997G>A

Variant summary

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

The ENST00000698884.1(ENSG00000250167):​n.496+41997G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 152,130 control chromosomes in the GnomAD database, including 19,709 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 0.48 (19709 hom., cov: 33)
• Consequence: ENSG00000250167 ENST00000698884.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0950
• Publications: 1 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.747 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+41997G>A		intron_variant	Intron 3 of 5
SLC25A48	ENST00000698885.1	n.364+19010G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72179 AN: 152012 Hom.: 19660 Cov.: 33

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.475 AC: 72281 AN: 152130 Hom.: 19709 Cov.: 33 AF XY: 0.468 AC XY: 34834 AN XY: 74380

African (AFR) AF: 0.754 AC: 31298 AN: 41504

American (AMR) AF: 0.374 AC: 5717 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1323 AN: 3468

East Asian (EAS) AF: 0.390 AC: 2016 AN: 5168

South Asian (SAS) AF: 0.533 AC: 2572 AN: 4828

European-Finnish (FIN) AF: 0.249 AC: 2632 AN: 10568

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.374 AC: 25440 AN: 67984

Other (OTH) AF: 0.451 AC: 952 AN: 2112

Alfa AF: 0.422 Hom.: 1865

Bravo AF: 0.492

Asia WGS AF: 0.492 AC: 1712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.55
PhyloP100		0.095

Splicing

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

Other links and lift over

dbSNP: rs6596238; hg19: chr5-134864456;