rs3134269

chr8-103409674-C-T

Variant summary

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

The NM_030780.5(SLC25A32):c.155-1890G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.053 in 152,274 control chromosomes in the GnomAD database, including 272 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 0.053 (272 hom., cov: 32)
• Consequence: SLC25A32 NM_030780.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

Genes affected

SLC25A32 (HGNC:29683): (solute carrier family 25 member 32) This gene encodes a member of the P(I/L)W subfamily of mitochondrial carrier family transport proteins. The encoded protein transports folate across the inner mitochondrial membrane. Alternatively spliced transcript variants have been described. [provided by RefSeq, Mar 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC25A32	NM_030780.5	c.155-1890G>A		intron_variant		ENST00000297578.9
SLC25A32	NR_102337.2	n.325-1890G>A		intron_variant, non_coding_transcript_variant
SLC25A32	NR_102338.2	n.434-1890G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC25A32	ENST00000297578.9	c.155-1890G>A		intron_variant		1	NM_030780.5	P1

Frequencies

GnomAD3 genomes AF: 0.0530 AC: 8067 AN: 152156 Hom.: 272 Cov.: 32

Gnomad AFR AF: 0.0232

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0515

Gnomad ASJ AF: 0.0524

Gnomad EAS AF: 0.00712

Gnomad SAS AF: 0.0149

Gnomad FIN AF: 0.0484

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0782

Gnomad OTH AF: 0.0674

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

GnomAD4 genome AF: 0.0530 AC: 8066 AN: 152274 Hom.: 272 Cov.: 32 AF XY: 0.0511 AC XY: 3802 AN XY: 74462

Gnomad4 AFR AF: 0.0232

Gnomad4 AMR AF: 0.0514

Gnomad4 ASJ AF: 0.0524

Gnomad4 EAS AF: 0.00714

Gnomad4 SAS AF: 0.0149

Gnomad4 FIN AF: 0.0484

Gnomad4 NFE AF: 0.0782

Gnomad4 OTH AF: 0.0662

Alfa AF: 0.0680 Hom.: 163

Bravo AF: 0.0528

Asia WGS AF: 0.0140 AC: 49 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.61
Dann	Benign	0.47

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: rs3134269; hg19: chr8-104421902;