rs1400816

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003705.5(SLC25A12):​c.930+2630T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.815 in 152,196 control chromosomes in the GnomAD database, including 51,740 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 0.82 ( 51740 hom., cov: 31)

Consequence

SLC25A12
NM_003705.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.346
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC25A12NM_003705.5 linkuse as main transcriptc.930+2630T>G intron_variant ENST00000422440.7
SLC25A12XM_047446142.1 linkuse as main transcriptc.657+2630T>G intron_variant
SLC25A12NR_047549.2 linkuse as main transcriptn.844+2630T>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC25A12ENST00000422440.7 linkuse as main transcriptc.930+2630T>G intron_variant 1 NM_003705.5 P1O75746-1
SLC25A12ENST00000263812.8 linkuse as main transcriptc.*550+2630T>G intron_variant, NMD_transcript_variant 2
SLC25A12ENST00000485880.1 linkuse as main transcriptn.458+2630T>G intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.816
AC:
124054
AN:
152078
Hom.:
51734
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.636
Gnomad AMI
AF:
0.911
Gnomad AMR
AF:
0.758
Gnomad ASJ
AF:
0.904
Gnomad EAS
AF:
0.911
Gnomad SAS
AF:
0.845
Gnomad FIN
AF:
0.887
Gnomad MID
AF:
0.905
Gnomad NFE
AF:
0.911
Gnomad OTH
AF:
0.840
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.815
AC:
124099
AN:
152196
Hom.:
51740
Cov.:
31
AF XY:
0.815
AC XY:
60678
AN XY:
74414
show subpopulations
Gnomad4 AFR
AF:
0.635
Gnomad4 AMR
AF:
0.758
Gnomad4 ASJ
AF:
0.904
Gnomad4 EAS
AF:
0.911
Gnomad4 SAS
AF:
0.845
Gnomad4 FIN
AF:
0.887
Gnomad4 NFE
AF:
0.911
Gnomad4 OTH
AF:
0.834
Alfa
AF:
0.898
Hom.:
97224
Bravo
AF:
0.800
Asia WGS
AF:
0.851
AC:
2963
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
8.9
DANN
Benign
0.81

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1400816; hg19: chr2-172680678; API