5-135671865-A-G

Position:

• chr5-135671865-A-G

Variant summary

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

The NM_001349335.2(SLC25A48):​c.-521+36909A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 132,482 control chromosomes in the GnomAD database, including 27,819 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 0.68 (27819 hom., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: SLC25A48 NM_001349335.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.878

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]

SLC25A48 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC25A48	NM_001349335.2	c.-521+36909A>G		intron_variant			NP_001336264.1
SLC25A48	NM_001349345.2	c.-521+36909A>G		intron_variant			NP_001336274.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC25A48	ENST00000646290.1	c.-521+36909A>G		intron_variant				ENSP00000493514.1
SLC25A48	ENST00000647391.1	n.829+118A>G		intron_variant
SLC25A48	ENST00000698885.1	n.365-89159A>G		intron_variant
SLC25A48	ENST00000698886.1	n.751+36909A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.678 AC: 89789 AN: 132404 Hom.: 27836 Cov.: 21

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.822

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.678 AC: 89790 AN: 132482 Hom.: 27819 Cov.: 21 AF XY: 0.676 AC XY: 43140 AN XY: 63776

Gnomad4 AFR AF: 0.629

Gnomad4 AMR AF: 0.657

Gnomad4 ASJ AF: 0.767

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.728

Gnomad4 NFE AF: 0.709

Gnomad4 OTH AF: 0.689

Alfa AF: 0.717 Hom.: 12691

Bravo AF: 0.673

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.51
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2067000; hg19: chr5-135007554;