8-144528767-C-A

Variant summary

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

The NM_001001795.2(C8orf82):​c.150G>T​(p.Gln50His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000283 in 1,413,378 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000013 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0000016 ( 0 hom. )

Consequence

C8orf82
NM_001001795.2 missense

Scores

6
12

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.0780
Variant links:
Genes affected
C8orf82 (HGNC:33826): (chromosome 8 open reading frame 82)

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=0.16790584).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
C8orf82NM_001001795.2 linkc.150G>T p.Gln50His missense_variant Exon 1 of 3 ENST00000524821.6 NP_001001795.1 Q6P1X6-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
C8orf82ENST00000524821.6 linkc.150G>T p.Gln50His missense_variant Exon 1 of 3 1 NM_001001795.2 ENSP00000436621.1 Q6P1X6-1

Frequencies

GnomAD3 genomes
AF:
0.0000133
AC:
2
AN:
150034
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000132
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
AF:
0.00000158
AC:
2
AN:
1263344
Hom.:
0
Cov.:
35
AF XY:
0.00
AC XY:
0
AN XY:
613832
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000496
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:
9.87e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000133
AC:
2
AN:
150034
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
73252
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.000132
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:
0.0000302
ExAC
AF:
0.0000431
AC:
5

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Sep 16, 2021
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.150G>T (p.Q50H) alteration is located in exon 1 (coding exon 1) of the C8orf82 gene. This alteration results from a G to T substitution at nucleotide position 150, causing the glutamine (Q) at amino acid position 50 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.40
BayesDel_addAF
Benign
-0.0065
T
BayesDel_noAF
Benign
-0.25
CADD
Benign
22
DANN
Uncertain
1.0
DEOGEN2
Benign
0.11
T;T
Eigen
Benign
-0.036
Eigen_PC
Benign
-0.038
FATHMM_MKL
Benign
0.63
D
LIST_S2
Uncertain
0.92
.;D
M_CAP
Uncertain
0.11
D
MetaRNN
Benign
0.17
T;T
MetaSVM
Benign
-0.85
T
MutationAssessor
Benign
1.7
L;.
PROVEAN
Uncertain
-4.2
D;D
REVEL
Benign
0.14
Sift
Benign
0.049
D;D
Sift4G
Uncertain
0.0080
D;D
Polyphen
1.0
D;.
Vest4
0.42
MutPred
0.31
Loss of sheet (P = 0.0357);Loss of sheet (P = 0.0357);
MVP
0.099
MPC
1.5
ClinPred
0.95
D
GERP RS
1.2
Varity_R
0.39
gMVP
0.72

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: rs777942397; hg19: chr8-145754151; API