rs182425183

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_015492.5(C15orf39):​c.1118C>G​(p.Pro373Arg) 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. 13/20 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. P373L) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 29)

Consequence

C15orf39
NM_015492.5 missense

Scores

1
3
14

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.27
Variant links:
Genes affected
C15orf39 (HGNC:24497): (chromosome 15 open reading frame 39) Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.22842804).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
C15orf39NM_015492.5 linkc.1118C>G p.Pro373Arg missense_variant Exon 2 of 3 ENST00000394987.5 NP_056307.3 Q6ZRI6-1
C15orf39XM_047432864.1 linkc.1118C>G p.Pro373Arg missense_variant Exon 3 of 4 XP_047288820.1
C15orf39XM_047432865.1 linkc.284C>G p.Pro95Arg missense_variant Exon 4 of 5 XP_047288821.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
C15orf39ENST00000394987.5 linkc.1118C>G p.Pro373Arg missense_variant Exon 2 of 3 1 NM_015492.5 ENSP00000378438.4 Q6ZRI6-1
C15orf39ENST00000567617.1 linkc.1118C>G p.Pro373Arg missense_variant Exon 1 of 2 1 ENSP00000458025.1 Q6ZRI6-2
C15orf39ENST00000360639.6 linkc.1118C>G p.Pro373Arg missense_variant Exon 2 of 3 2 ENSP00000353854.2 Q6ZRI6-1
C15orf39ENST00000565074.1 linkc.722C>G p.Pro241Arg missense_variant Exon 1 of 1 6 ENSP00000454405.1 H3BMJ2

Frequencies

GnomAD3 genomes
Cov.:
29
GnomAD4 exome
Cov.:
70
GnomAD4 genome
Cov.:
29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.17
BayesDel_addAF
Benign
-0.0064
T
BayesDel_noAF
Benign
-0.25
CADD
Benign
22
DANN
Uncertain
0.98
DEOGEN2
Benign
0.056
T;T;.
Eigen
Benign
0.033
Eigen_PC
Benign
-0.065
FATHMM_MKL
Benign
0.57
D
LIST_S2
Benign
0.73
.;T;T
M_CAP
Benign
0.057
D
MetaRNN
Benign
0.23
T;T;T
MetaSVM
Benign
-0.59
T
MutationAssessor
Benign
1.9
L;L;L
PROVEAN
Pathogenic
-4.8
D;D;D
REVEL
Benign
0.24
Sift
Uncertain
0.0040
D;D;D
Sift4G
Uncertain
0.0050
D;D;D
Polyphen
0.90
P;P;.
Vest4
0.36
MutPred
0.35
Gain of solvent accessibility (P = 0.0055);Gain of solvent accessibility (P = 0.0055);Gain of solvent accessibility (P = 0.0055);
MVP
0.15
MPC
0.77
ClinPred
0.97
D
GERP RS
4.8
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.24
gMVP
0.35

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: rs182425183; hg19: chr15-75499507; API