rs6596271

Positions:

• chr5-135885140-A-G
• chr5-135885140-A-T

Variant summary

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

The NM_001349336.2(SLC25A48):​c.*8-2892A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0711 in 152,178 control chromosomes in the GnomAD database, including 489 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 0.071 (489 hom., cov: 32)
• Consequence: SLC25A48 NM_001349336.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC25A48	NM_001349336.2	c.*8-2892A>G		intron_variant		ENST00000681962.1	NP_001336265.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC25A48	ENST00000681962.1	c.*8-2892A>G		intron_variant			NM_001349336.2	ENSP00000506858.1
SLC25A48	ENST00000412661.3	c.422-2892A>G		intron_variant		1		ENSP00000413049.2
SLC25A48	ENST00000646290.1	c.*8-2892A>G		intron_variant				ENSP00000493514.1

Frequencies

GnomAD3 genomes AF: 0.0709 AC: 10784 AN: 152060 Hom.: 482 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0575

Gnomad ASJ AF: 0.0567

Gnomad EAS AF: 0.0365

Gnomad SAS AF: 0.0298

Gnomad FIN AF: 0.0338

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0550

Gnomad OTH AF: 0.0771

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

GnomAD4 genome AF: 0.0711 AC: 10813 AN: 152178 Hom.: 489 Cov.: 32 AF XY: 0.0689 AC XY: 5125 AN XY: 74416

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.0574

Gnomad4 ASJ AF: 0.0567

Gnomad4 EAS AF: 0.0366

Gnomad4 SAS AF: 0.0296

Gnomad4 FIN AF: 0.0338

Gnomad4 NFE AF: 0.0550

Gnomad4 OTH AF: 0.0763

Alfa AF: 0.0588 Hom.: 425

Bravo AF: 0.0745

Asia WGS AF: 0.0410 AC: 144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.034
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6596271; hg19: chr5-135220829;