17-744917-G-C

Variant summary

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

The NM_015721.3(GEMIN4):ā€‹c.3126C>Gā€‹(p.Ile1042Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,146 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 34)
Exomes š‘“: 6.8e-7 ( 0 hom. )

Consequence

GEMIN4
NM_015721.3 missense

Scores

2
17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.235
Variant links:
Genes affected
GEMIN4 (HGNC:15717): (gem nuclear organelle associated protein 4) The product of this gene is part of a large complex localized to the cytoplasm, nucleoli, and to discrete nuclear bodies called Gemini bodies (gems). The complex functions in spliceosomal snRNP assembly in the cytoplasm, and regenerates spliceosomes required for pre-mRNA splicing in the nucleus. The encoded protein directly interacts with a DEAD box protein and several spliceosome core proteins. Alternatively spliced transcript variants have been described, but their biological validity has not been determined. [provided by RefSeq, Jul 2008]

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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=0.10731882).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GEMIN4NM_015721.3 linkc.3126C>G p.Ile1042Met missense_variant Exon 2 of 2 ENST00000319004.6 NP_056536.2 P57678Q8WUM5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GEMIN4ENST00000319004.6 linkc.3126C>G p.Ile1042Met missense_variant Exon 2 of 2 1 NM_015721.3 ENSP00000321706.5 P57678
GEMIN4ENST00000576778.1 linkc.3093C>G p.Ile1031Met missense_variant Exon 1 of 1 6 ENSP00000459565.1 I3L2C7

Frequencies

GnomAD3 genomes
Cov.:
34
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461146
Hom.:
0
Cov.:
32
AF XY:
0.00000138
AC XY:
1
AN XY:
726832
show subpopulations
Gnomad4 AFR exome
AF:
0.0000299
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:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.13
BayesDel_addAF
Benign
-0.24
T
BayesDel_noAF
Benign
-0.58
CADD
Benign
1.4
DANN
Benign
0.97
DEOGEN2
Benign
0.024
T;.
Eigen
Benign
-0.63
Eigen_PC
Benign
-0.77
FATHMM_MKL
Benign
0.22
N
LIST_S2
Benign
0.72
T;T
M_CAP
Benign
0.015
T
MetaRNN
Benign
0.11
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.90
L;.
PrimateAI
Benign
0.38
T
PROVEAN
Benign
-1.4
N;.
REVEL
Benign
0.078
Sift
Uncertain
0.0070
D;.
Sift4G
Uncertain
0.010
D;D
Polyphen
0.94
P;.
Vest4
0.36
MutPred
0.31
Loss of catalytic residue at P1044 (P = 0.036);.;
MVP
0.19
MPC
0.34
ClinPred
0.58
D
GERP RS
-2.2
Varity_R
0.15
gMVP
0.17

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: rs1045481; hg19: chr17-648157; API