22-29060794-C-T
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_015370.2(C22orf31):c.53G>A(p.Arg18Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000669 in 1,613,652 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00049 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00069 ( 1 hom. )
Consequence
C22orf31
NM_015370.2 missense
NM_015370.2 missense
Scores
3
2
13
Clinical Significance
Conservation
PhyloP100: 1.18
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.018286496).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
C22orf31 | NM_015370.2 | c.53G>A | p.Arg18Gln | missense_variant | 2/3 | ENST00000216071.5 | NP_056185.1 | |
C22orf31 | NM_001386866.1 | c.-71G>A | 5_prime_UTR_variant | 2/3 | NP_001373795.1 | |||
C22orf31 | XM_017028741.2 | c.-71G>A | 5_prime_UTR_variant | 2/3 | XP_016884230.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000500 AC: 76AN: 152036Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000609 AC: 153AN: 251414Hom.: 0 AF XY: 0.000633 AC XY: 86AN XY: 135864
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GnomAD4 exome AF: 0.000687 AC: 1004AN: 1461498Hom.: 1 Cov.: 33 AF XY: 0.000697 AC XY: 507AN XY: 727084
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GnomAD4 genome AF: 0.000493 AC: 75AN: 152154Hom.: 1 Cov.: 32 AF XY: 0.000457 AC XY: 34AN XY: 74368
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | New York Genome Center | Jan 28, 2020 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Pathogenic
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
PROVEAN
Uncertain
D
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
Find out detailed SpliceAI scores and Pangolin per-transcript scores at