rs6596238

chr5-135528766-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000698884.1(ENSG00000250167):n.496+41997G>A variant causes a intron, non coding transcript 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: ENST00000698884.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0950

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 -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000698884.1	n.496+41997G>A		intron_variant, non_coding_transcript_variant
SLC25A48	ENST00000698885.1	n.364+19010G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.754

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.451

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6596238; hg19: chr5-134864456;