rs991080602

Variant summary

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

The NM_024093.3(C2orf49):ā€‹c.82C>Gā€‹(p.Leu28Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000704 in 141,960 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: š‘“ 0.0000070 ( 0 hom., cov: 28)

Consequence

C2orf49
NM_024093.3 missense

Scores

3
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.58
Variant links:
Genes affected
C2orf49 (HGNC:28772): (chromosome 2 open reading frame 49) Predicted to be involved in embryonic morphogenesis. Located in nucleus. Part of tRNA-splicing ligase complex. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

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=0.2634575).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
C2orf49NM_024093.3 linkc.82C>G p.Leu28Val missense_variant Exon 1 of 4 ENST00000258457.7 NP_076998.1 Q9BVC5-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
C2orf49ENST00000258457.7 linkc.82C>G p.Leu28Val missense_variant Exon 1 of 4 1 NM_024093.3 ENSP00000258457.2 Q9BVC5-1
C2orf49ENST00000410049.1 linkc.82C>G p.Leu28Val missense_variant Exon 1 of 5 1 ENSP00000386361.1 C9J4K0

Frequencies

GnomAD3 genomes
AF:
0.00000704
AC:
1
AN:
141960
Hom.:
0
Cov.:
28
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000714
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
Cov.:
44
GnomAD4 genome
AF:
0.00000704
AC:
1
AN:
141960
Hom.:
0
Cov.:
28
AF XY:
0.00
AC XY:
0
AN XY:
68730
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.0000714
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.16
BayesDel_addAF
Benign
-0.082
T
BayesDel_noAF
Benign
-0.36
CADD
Pathogenic
29
DANN
Uncertain
1.0
DEOGEN2
Benign
0.022
T;T
Eigen
Benign
0.18
Eigen_PC
Benign
0.18
FATHMM_MKL
Benign
0.60
D
LIST_S2
Benign
0.84
T;T
M_CAP
Uncertain
0.087
D
MetaRNN
Benign
0.26
T;T
MetaSVM
Benign
-0.75
T
MutationAssessor
Uncertain
2.3
M;.
PROVEAN
Benign
-1.4
N;N
REVEL
Benign
0.095
Sift
Benign
0.053
T;T
Sift4G
Benign
0.10
T;T
Polyphen
0.91
P;.
Vest4
0.39
MutPred
0.28
Gain of relative solvent accessibility (P = 0.09);Gain of relative solvent accessibility (P = 0.09);
MVP
0.38
MPC
0.20
ClinPred
0.96
D
GERP RS
4.7
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.47
gMVP
0.16

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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: rs991080602; hg19: chr2-105954126; API