4-76313223-G-T
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001394954.1(CCDC158):c.3301C>A(p.Gln1101Lys) variant causes a missense change. The variant allele was found at a frequency of 0.000538 in 1,606,090 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Genomes: 𝑓 0.00045 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00055 ( 1 hom. )
Consequence
CCDC158
NM_001394954.1 missense
NM_001394954.1 missense
Scores
3
5
11
Clinical Significance
Conservation
PhyloP100: 6.34
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCDC158 | NM_001394954.1 | c.3301C>A | p.Gln1101Lys | missense_variant | 25/25 | ENST00000682701.1 | NP_001381883.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC158 | ENST00000682701.1 | c.3301C>A | p.Gln1101Lys | missense_variant | 25/25 | NM_001394954.1 | ENSP00000507278.1 | |||
CCDC158 | ENST00000504667.2 | n.3167C>A | non_coding_transcript_exon_variant | 13/13 | 1 | |||||
CCDC158 | ENST00000388914.7 | c.3289C>A | p.Gln1097Lys | missense_variant | 24/24 | 5 | ENSP00000373566.2 |
Frequencies
GnomAD3 genomes AF: 0.000447 AC: 68AN: 152036Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000287 AC: 70AN: 243726Hom.: 0 AF XY: 0.000318 AC XY: 42AN XY: 132238
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GnomAD4 exome AF: 0.000547 AC: 796AN: 1454054Hom.: 1 Cov.: 27 AF XY: 0.000503 AC XY: 364AN XY: 723454
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GnomAD4 genome AF: 0.000447 AC: 68AN: 152036Hom.: 0 Cov.: 33 AF XY: 0.000364 AC XY: 27AN XY: 74266
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Department of Pathology and Laboratory Medicine, Sinai Health System | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Benign
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Pathogenic
D
Sift4G
Pathogenic
D
Polyphen
D
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AL_spliceai
Position offset: 23
Find out detailed SpliceAI scores and Pangolin per-transcript scores at