X-14020459-C-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001042479.2(GEMIN8):ā€‹c.91G>Cā€‹(p.Ala31Pro) variant causes a missense change. The variant allele was found at a frequency of 0.00000498 in 1,205,692 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: š‘“ 0.0000089 ( 0 hom., 0 hem., cov: 23)
Exomes š‘“: 0.0000046 ( 0 hom. 2 hem. )

Consequence

GEMIN8
NM_001042479.2 missense

Scores

5
10
2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.98
Variant links:
Genes affected
GEMIN8 (HGNC:26044): (gem nuclear organelle associated protein 8) The protein encoded by this gene is part of the SMN complex, which is necessary for spliceosomal snRNP assembly in the cytoplasm and pre-mRNA splicing in the nucleus. The encoded protein binds to both SMN1 and the GEMIN6/GEMIN7 heterodimer, mediating their interaction. This protein is found in nuclear Gemini of Cajal bodies (gems) and in the cytoplasm. Three transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, May 2010]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2
High Hemizygotes in GnomAdExome4 at 2 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GEMIN8NM_001042479.2 linkc.91G>C p.Ala31Pro missense_variant Exon 4 of 5 ENST00000680255.1 NP_001035944.1 Q9NWZ8A0A024RBX2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GEMIN8ENST00000680255.1 linkc.91G>C p.Ala31Pro missense_variant Exon 4 of 5 NM_001042479.2 ENSP00000505429.1 Q9NWZ8

Frequencies

GnomAD3 genomes
AF:
0.00000893
AC:
1
AN:
112025
Hom.:
0
Cov.:
23
AF XY:
0.00
AC XY:
0
AN XY:
34185
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
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:
0.0000188
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00000457
AC:
5
AN:
1093667
Hom.:
0
Cov.:
28
AF XY:
0.00000557
AC XY:
2
AN XY:
359173
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:
0.00000597
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00000893
AC:
1
AN:
112025
Hom.:
0
Cov.:
23
AF XY:
0.00
AC XY:
0
AN XY:
34185
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000188
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
Pathogenic
0.98
BayesDel_addAF
Pathogenic
0.26
D
BayesDel_noAF
Pathogenic
0.14
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Benign
0.17
T;T;T
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Uncertain
0.87
.;D;D
M_CAP
Pathogenic
0.33
D
MetaRNN
Uncertain
0.54
D;D;D
MetaSVM
Uncertain
-0.28
T
MutationAssessor
Uncertain
2.5
M;M;.
PrimateAI
Uncertain
0.50
T
PROVEAN
Uncertain
-2.9
D;D;D
REVEL
Uncertain
0.34
Sift
Uncertain
0.012
D;D;D
Sift4G
Uncertain
0.040
D;D;D
Polyphen
1.0
D;D;.
Vest4
0.82
MutPred
0.47
Loss of MoRF binding (P = 0.0602);Loss of MoRF binding (P = 0.0602);Loss of MoRF binding (P = 0.0602);
MVP
0.54
MPC
1.3
ClinPred
0.99
D
GERP RS
5.1
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.92
gMVP
0.85

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: rs61740319; hg19: chrX-14038578; API