rs31263

chr5-135633272-G-C

Variant summary

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

The ENST00000698884.1(ENSG00000250167):n.637-1497G>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 151,972 control chromosomes in the GnomAD database, including 6,634 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 (6634 hom., cov: 31)
• Consequence: ENST00000698884.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

Genes affected

(HGNC:):

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC25A48	NM_001349335.2	c.-708-1497G>C		intron_variant
SLC25A48	NM_001349345.2	c.-708-1497G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000698884.1	n.637-1497G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43121 AN: 151854 Hom.: 6619 Cov.: 31

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.284 AC: 43164 AN: 151972 Hom.: 6634 Cov.: 31 AF XY: 0.290 AC XY: 21514 AN XY: 74266

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.593

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.286

Alfa AF: 0.278 Hom.: 719

Bravo AF: 0.284

Asia WGS AF: 0.461 AC: 1599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	7.6
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs31263; hg19: chr5-134968962;