rs908670

Variant names:

• chr2-171833670-T-C
• rs908670
• NM_003705.5:c.845+293A>G

Variant summary

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

The NM_003705.5(SLC25A12):​c.845+293A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 151,900 control chromosomes in the GnomAD database, including 6,672 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 0.29 (6672 hom., cov: 31)
• Consequence: SLC25A12 NM_003705.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 7 publications found

Genes affected

SLC25A12 (HGNC:10982): (solute carrier family 25 member 12) This gene encodes a calcium-binding mitochondrial carrier protein. The encoded protein localizes to the mitochondria and is involved in the exchange of aspartate for glutamate across the inner mitochondrial membrane. Polymorphisms in this gene may be associated with autism, and mutations in this gene may also be a cause of global cerebral hypomyelination. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Apr 2012]

SLC25A12 Gene-Disease associations (from GenCC):

• developmental and epileptic encephalopathy, 39

  Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, Ambry Genetics
• mitochondrial disease

  Inheritance: AR Classification: MODERATE Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC25A12	NM_003705.5	c.845+293A>G		intron_variant	Intron 8 of 17	ENST00000422440.7	NP_003696.2
SLC25A12	NR_047549.2	n.759+293A>G		intron_variant	Intron 7 of 16
SLC25A12	XM_047446142.1	c.572+293A>G		intron_variant	Intron 6 of 15		XP_047302098.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC25A12	ENST00000422440.7	c.845+293A>G		intron_variant	Intron 8 of 17	1	NM_003705.5	ENSP00000388658.2
SLC25A12	ENST00000263812.8	n.*465+293A>G		intron_variant	Intron 7 of 16	2		ENSP00000263812.4
SLC25A12	ENST00000485880.1	n.373+293A>G		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.290 AC: 43971 AN: 151782 Hom.: 6669 Cov.: 31

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.290 AC: 43998 AN: 151900 Hom.: 6672 Cov.: 31 AF XY: 0.283 AC XY: 21037 AN XY: 74248

African (AFR) AF: 0.370 AC: 15315 AN: 41360

American (AMR) AF: 0.247 AC: 3771 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 911 AN: 3468

East Asian (EAS) AF: 0.189 AC: 977 AN: 5160

South Asian (SAS) AF: 0.176 AC: 847 AN: 4816

European-Finnish (FIN) AF: 0.204 AC: 2153 AN: 10548

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19132 AN: 67956

Other (OTH) AF: 0.280 AC: 592 AN: 2114

Alfa AF: 0.280 Hom.: 3052

Bravo AF: 0.298

Asia WGS AF: 0.231 AC: 804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.48
PhyloP100		-0.055
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: rs908670; hg19: chr2-172690180;