NM_001349335.2:c.-521+36909A>G

Variant names:

• chr5-135671865-A-G
• rs2067000
• NM_001349335.2:c.-521+36909A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001349335.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A48	NM_001349335.2		c.-521+36909A>G		intron	N/A	NP_001336264.1	J3KQI1
	SLC25A48	NM_001349345.2		c.-521+36909A>G		intron	N/A	NP_001336274.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A48	ENST00000646290.1		c.-521+36909A>G		intron	N/A	ENSP00000493514.1	J3KQI1
	SLC25A48	ENST00000647391.1		n.829+118A>G		intron	N/A
	SLC25A48	ENST00000698885.1		n.365-89159A>G		intron	N/A

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

African (AFR) AF: 0.629 AC: 22096 AN: 35116

American (AMR) AF: 0.657 AC: 8122 AN: 12366

Ashkenazi Jewish (ASJ) AF: 0.767 AC: 2474 AN: 3226

East Asian (EAS) AF: 0.461 AC: 1703 AN: 3694

South Asian (SAS) AF: 0.663 AC: 2676 AN: 4034

European-Finnish (FIN) AF: 0.728 AC: 6211 AN: 8530

Middle Eastern (MID) AF: 0.812 AC: 224 AN: 276

European-Non Finnish (NFE) AF: 0.709 AC: 44377 AN: 62600

Other (OTH) AF: 0.689 AC: 1236 AN: 1794

Alfa AF: 0.720 Hom.: 14833

Bravo AF: 0.673

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.51
DANN	Benign	0.41
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs2067000; hg19: chr5-135007554;