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GeneBe

rs17803441

Positions:

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_030780.5(SLC25A32):​c.350G>C​(p.Arg117Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R117H) has been classified as Benign.

Frequency

Genomes: not found (cov: 32)

Consequence

SLC25A32
NM_030780.5 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0350
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
?
    PM2 - Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
Very rare variant in population databases, with high coverage;
BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (MetaRNN=0.027296335).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC25A32NM_030780.5 linkuse as main transcriptc.350G>C p.Arg117Pro missense_variant 3/7 ENST00000297578.9
SLC25A32NR_102338.2 linkuse as main transcriptn.629G>C non_coding_transcript_exon_variant 4/8
SLC25A32NR_102337.2 linkuse as main transcriptn.476-1493G>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC25A32ENST00000297578.9 linkuse as main transcriptc.350G>C p.Arg117Pro missense_variant 3/71 NM_030780.5 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
Cov.:
32
GnomAD4 exome
Cov.:
29
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.19
BayesDel_addAF
Benign
-0.15
T
BayesDel_noAF
Benign
-0.45
CADD
Benign
11
DANN
Benign
0.91
DEOGEN2
Benign
0.045
T;.
Eigen
Benign
-1.0
Eigen_PC
Benign
-0.94
FATHMM_MKL
Benign
0.14
N
LIST_S2
Benign
0.74
T;T
M_CAP
Benign
0.024
T
MetaRNN
Benign
0.027
T;T
MetaSVM
Benign
-0.97
T
MutationAssessor
Benign
-0.61
N;.
MutationTaster
Benign
1.0
N;N
PrimateAI
Benign
0.29
T
PROVEAN
Benign
2.3
N;.
REVEL
Benign
0.15
Sift
Benign
0.40
T;.
Sift4G
Benign
0.34
T;.
Polyphen
0.0020
B;.
Vest4
0.15
MutPred
0.26
Loss of solvent accessibility (P = 0.0703);.;
MVP
0.71
MPC
0.45
ClinPred
0.14
T
GERP RS
-2.2
Varity_R
0.088
gMVP
0.79

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr8-104417045; API