rs3098241

Variant names:

• chr8-103413076-A-G
• rs3098241
• NM_030780.5:c.154+1708T>C

Variant summary

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

The NM_030780.5(SLC25A32):​c.154+1708T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,086 control chromosomes in the GnomAD database, including 1,966 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 0.15 (1966 hom., cov: 32)
• Consequence: SLC25A32 NM_030780.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 12 publications found

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]

SLC25A32 Gene-Disease associations (from GenCC):

• exercise intolerance, riboflavin-responsive

  Inheritance: AR, Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine

ENSG00000285982 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC25A32	NM_030780.5	c.154+1708T>C		intron_variant	Intron 1 of 6	ENST00000297578.9	NP_110407.2
SLC25A32	NR_102337.2	n.324+1708T>C		intron_variant	Intron 1 of 5
SLC25A32	NR_102338.2	n.433+347T>C		intron_variant	Intron 2 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC25A32	ENST00000297578.9	c.154+1708T>C		intron_variant	Intron 1 of 6	1	NM_030780.5	ENSP00000297578.4
ENSG00000285982	ENST00000649416.1	c.2-5292T>C		intron_variant	Intron 3 of 8			ENSP00000496817.1

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23343 AN: 151968 Hom.: 1961 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.154 AC: 23361 AN: 152086 Hom.: 1966 Cov.: 32 AF XY: 0.161 AC XY: 11983 AN XY: 74340

African (AFR) AF: 0.124 AC: 5131 AN: 41500

American (AMR) AF: 0.175 AC: 2677 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 378 AN: 3472

East Asian (EAS) AF: 0.335 AC: 1728 AN: 5158

South Asian (SAS) AF: 0.225 AC: 1082 AN: 4816

European-Finnish (FIN) AF: 0.228 AC: 2406 AN: 10566

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9468 AN: 67970

Other (OTH) AF: 0.147 AC: 310 AN: 2110

Alfa AF: 0.144 Hom.: 2531

Bravo AF: 0.148

Asia WGS AF: 0.286 AC: 993 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	2.8
DANN	Benign	0.61
PhyloP100		0.12
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: rs3098241; hg19: chr8-104425304;