NM_006358.4:c.733G>C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_006358.4(SLC25A17):​c.733G>C​(p.Gly245Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,280 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 6.8e-7 ( 0 hom. )

Consequence

SLC25A17
NM_006358.4 missense

Scores

3
7
9

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.16
Variant links:
Genes affected
SLC25A17 (HGNC:10987): (solute carrier family 25 member 17) This gene encodes a peroxisomal membrane protein that belongs to the family of mitochondrial solute carriers. It is expressed in the liver, and is likely involved in transport. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC25A17NM_006358.4 linkc.733G>C p.Gly245Arg missense_variant Exon 8 of 9 ENST00000435456.7 NP_006349.1 O43808

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC25A17ENST00000435456.7 linkc.733G>C p.Gly245Arg missense_variant Exon 8 of 9 1 NM_006358.4 ENSP00000390722.2 O43808

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461280
Hom.:
0
Cov.:
29
AF XY:
0.00
AC XY:
0
AN XY:
727030
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.00e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.32
BayesDel_addAF
Pathogenic
0.44
D
BayesDel_noAF
Pathogenic
0.40
CADD
Uncertain
25
DANN
Uncertain
0.99
DEOGEN2
Benign
0.15
T;.;T
Eigen
Benign
-0.27
Eigen_PC
Benign
-0.14
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Uncertain
0.96
D;D;D
M_CAP
Uncertain
0.13
D
MetaRNN
Uncertain
0.64
D;D;D
MetaSVM
Benign
-0.48
T
MutationAssessor
Benign
1.8
L;.;.
PrimateAI
Uncertain
0.72
T
PROVEAN
Benign
-2.1
N;D;N
REVEL
Uncertain
0.56
Sift
Uncertain
0.020
D;D;D
Sift4G
Benign
0.13
T;T;T
Polyphen
0.045
B;.;.
Vest4
0.77
MutPred
0.45
Gain of MoRF binding (P = 0.0086);.;.;
MVP
0.80
MPC
0.66
ClinPred
0.89
D
GERP RS
5.0
Varity_R
0.22
gMVP
0.74

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: chr22-41169984; API