5-135885140-A-G

Variant names:

• chr5-135885140-A-G
• rs6596271
• NM_001349336.2:c.*8-2892A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001349336.2. 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_001349336.2	MANE Select	c.*8-2892A>G		intron	N/A	NP_001336265.1
	SLC25A48	NM_001349335.2		c.*8-2892A>G		intron	N/A	NP_001336264.1
	SLC25A48	NM_145282.5		c.422-2892A>G		intron	N/A	NP_660325.4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A48	ENST00000681962.1	MANE Select	c.*8-2892A>G		intron	N/A	ENSP00000506858.1
	SLC25A48	ENST00000412661.3	TSL:1	c.422-2892A>G		intron	N/A	ENSP00000413049.2
	SLC25A48	ENST00000646290.1		c.*8-2892A>G		intron	N/A	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

African (AFR) AF: 0.123 AC: 5100 AN: 41492

American (AMR) AF: 0.0574 AC: 878 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0567 AC: 197 AN: 3472

East Asian (EAS) AF: 0.0366 AC: 189 AN: 5166

South Asian (SAS) AF: 0.0296 AC: 143 AN: 4824

European-Finnish (FIN) AF: 0.0338 AC: 359 AN: 10616

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0550 AC: 3742 AN: 67998

Other (OTH) AF: 0.0763 AC: 161 AN: 2110

Alfa AF: 0.0613 Hom.: 562

Bravo AF: 0.0745

Asia WGS AF: 0.0410 AC: 144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.034
DANN	Benign	0.30
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6596271; hg19: chr5-135220829;