chr13-45411570-G-A

Position:

• chr13-45411570-G-A

Variant summary

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

The ENST00000519676.6(SLC25A30):​c.-55-90C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 792,604 control chromosomes in the GnomAD database, including 56,873 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 0.31 (8864 hom., cov: 32)
  • Exomes 𝑓: 0.37 (48009 hom.)
• Consequence: SLC25A30 ENST00000519676.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.704

Genes affected

SLC25A30 (HGNC:27371): (solute carrier family 25 member 30) Although the outer mitochondrial membrane is permeable to many small metabolites, transport of solutes across the inner mitochondrial membrane is achieved by members of the mitochondrial carrier protein family, such as SLC25A30 (Haguenauer et al., 2005 [PubMed 15809292]).[supplied by OMIM, Mar 2008]

TPT1-AS1 (HGNC:43686): (TPT1 antisense RNA 1) Biomarker of malignant astrocytoma. [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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC25A30	NM_001010875.4	c.-55-90C>T		intron_variant		ENST00000519676.6	NP_001010875.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC25A30	ENST00000519676.6	c.-55-90C>T		intron_variant		1	NM_001010875.4	ENSP00000429168	P1
TPT1-AS1	ENST00000661291.1	n.458-5930G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47189 AN: 152008 Hom.: 8865 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.317

GnomAD4 exome AF: 0.371 AC: 237357 AN: 640478 Hom.: 48009 Cov.: 9 AF XY: 0.364 AC XY: 120945 AN XY: 332404

Gnomad4 AFR exome AF: 0.110

Gnomad4 AMR exome AF: 0.304

Gnomad4 ASJ exome AF: 0.387

Gnomad4 EAS exome AF: 0.108

Gnomad4 SAS exome AF: 0.210

Gnomad4 FIN exome AF: 0.423

Gnomad4 NFE exome AF: 0.426

Gnomad4 OTH exome AF: 0.352

GnomAD4 genome AF: 0.310 AC: 47178 AN: 152126 Hom.: 8864 Cov.: 32 AF XY: 0.306 AC XY: 22732 AN XY: 74374

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.313

Alfa AF: 0.400 Hom.: 9094

Bravo AF: 0.297

Asia WGS AF: 0.145 AC: 506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.87
DANN	Benign	0.64

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4941527; hg19: chr13-45985705;