chr5-135648666-G-A

Variant names:

• chr5-135648666-G-A
• rs801564
• ENST00000508452.1:n.2059C>T

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+13710G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 152,160 control chromosomes in the GnomAD database, including 6,334 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 0.28 (6334 hom., cov: 33)
  • Exomes 𝑓: 0.30 (0 hom.)
• Consequence: SLC25A48 NM_001349335.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.191
• Publications: 5 publications found

Genes affected

SLC25A48-AS1 (HGNC:27965): (SLC25A48 antisense RNA 1)

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.607 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+13710G>A		intron	N/A	NP_001336264.1	J3KQI1
	SLC25A48	NM_001349345.2		c.-521+13710G>A		intron	N/A	NP_001336274.1
	SLC25A48-AS1	NR_027127.1		n.*17C>T		downstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A48-AS1	ENST00000508452.1	TSL:1	n.2059C>T		non_coding_transcript_exon	Exon 3 of 3
	SLC25A48	ENST00000646290.1		c.-521+13710G>A		intron	N/A	ENSP00000493514.1	J3KQI1
	SLC25A48	ENST00000647391.1		n.745+13710G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41939 AN: 152032 Hom.: 6322 Cov.: 33

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.282

GnomAD4 exome AF: 0.300 AC: 3 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.300 AC XY: 3 AN XY: 10

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.300 AC: 3 AN: 10

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.276 AC: 41987 AN: 152150 Hom.: 6334 Cov.: 33 AF XY: 0.281 AC XY: 20920 AN XY: 74388

African (AFR) AF: 0.215 AC: 8911 AN: 41510

American (AMR) AF: 0.343 AC: 5249 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 673 AN: 3468

East Asian (EAS) AF: 0.625 AC: 3233 AN: 5170

South Asian (SAS) AF: 0.345 AC: 1664 AN: 4824

European-Finnish (FIN) AF: 0.310 AC: 3277 AN: 10576

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18202 AN: 67994

Other (OTH) AF: 0.288 AC: 607 AN: 2106

Alfa AF: 0.267 Hom.: 2909

Bravo AF: 0.279

Asia WGS AF: 0.456 AC: 1582 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.5
DANN	Benign	0.74
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs801564; hg19: chr5-134984355;