rs4941527

Variant names:

• chr13-45411570-G-A
• rs4941527
• NM_001010875.4:c.-55-90C>T

Your query was ambiguous. Multiple possible variants found:

• chr13-45411570-G-A
• chr13-45411570-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001010875.4(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 NM_001010875.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.704
• Publications: 9 publications found

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

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 = 0.423 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001010875.4. 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
	SLC25A30	NM_001010875.4	MANE Select	c.-55-90C>T		intron	N/A	NP_001010875.1	Q5SVS4-1
	SLC25A30	NM_001286806.2		c.-89-2496C>T		intron	N/A	NP_001273735.1	Q5SVS4-2
	SLC25A30	NM_001286807.2		c.-132-90C>T		intron	N/A	NP_001273736.1	B3KTE8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A30	ENST00000519676.6	TSL:1 MANE Select	c.-55-90C>T		intron	N/A	ENSP00000429168.1	Q5SVS4-1
	SLC25A30	ENST00000310862.11	TSL:1	n.-55-90C>T		intron	N/A	ENSP00000311856.7	D6RJI0
	SLC25A30	ENST00000857535.1		c.-145C>T		5_prime_UTR	Exon 1 of 9	ENSP00000527594.1

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

African (AFR) AF: 0.110 AC: 1900 AN: 17250

American (AMR) AF: 0.304 AC: 9675 AN: 31842

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 6971 AN: 18036

East Asian (EAS) AF: 0.108 AC: 3406 AN: 31556

South Asian (SAS) AF: 0.210 AC: 12115 AN: 57774

European-Finnish (FIN) AF: 0.423 AC: 16084 AN: 38052

Middle Eastern (MID) AF: 0.296 AC: 757 AN: 2554

European-Non Finnish (NFE) AF: 0.426 AC: 175035 AN: 410974

Other (OTH) AF: 0.352 AC: 11414 AN: 32440

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

African (AFR) AF: 0.112 AC: 4661 AN: 41520

American (AMR) AF: 0.338 AC: 5169 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1334 AN: 3470

East Asian (EAS) AF: 0.115 AC: 593 AN: 5178

South Asian (SAS) AF: 0.205 AC: 989 AN: 4834

European-Finnish (FIN) AF: 0.406 AC: 4286 AN: 10562

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.427 AC: 29035 AN: 67962

Other (OTH) AF: 0.313 AC: 660 AN: 2110

Alfa AF: 0.392 Hom.: 10326

Bravo AF: 0.297

Asia WGS AF: 0.145 AC: 506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.87
DANN	Benign	0.64
PhyloP100		-0.70
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4941527; hg19: chr13-45985705;