chr4-48988665-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_025087.3(CWH43):c.232A>G(p.Ile78Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00321 in 1,585,008 control chromosomes in the GnomAD database, including 72 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.014 ( 34 hom., cov: 32)
Exomes 𝑓: 0.0021 ( 38 hom. )
Consequence
CWH43
NM_025087.3 missense
NM_025087.3 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: 0.278
Genes affected
CWH43 (HGNC:26133): (cell wall biogenesis 43 C-terminal homolog) Predicted to be involved in GPI anchor biosynthetic process. Predicted to be integral component of membrane. Predicted to be active in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0067112744).
BP6
?
Variant 4-48988665-A-G is Benign according to our data. Variant chr4-48988665-A-G is described in ClinVar as [Benign]. Clinvar id is 775963.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0139 (2110/152298) while in subpopulation AFR AF= 0.0439 (1824/41550). AF 95% confidence interval is 0.0422. There are 34 homozygotes in gnomad4. There are 1022 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 33 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CWH43 | NM_025087.3 | c.232A>G | p.Ile78Val | missense_variant | 2/16 | ENST00000226432.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CWH43 | ENST00000226432.9 | c.232A>G | p.Ile78Val | missense_variant | 2/16 | 1 | NM_025087.3 | P1 | |
CWH43 | ENST00000513409.1 | c.151A>G | p.Ile51Val | missense_variant | 2/16 | 2 | |||
CWH43 | ENST00000514053.6 | c.232A>G | p.Ile78Val | missense_variant, NMD_transcript_variant | 2/14 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0139 AC: 2109AN: 152182Hom.: 33 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00438 AC: 988AN: 225618Hom.: 20 AF XY: 0.00350 AC XY: 426AN XY: 121878
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GnomAD4 exome AF: 0.00207 AC: 2972AN: 1432710Hom.: 38 Cov.: 28 AF XY: 0.00188 AC XY: 1340AN XY: 712338
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GnomAD4 genome ? AF: 0.0139 AC: 2110AN: 152298Hom.: 34 Cov.: 32 AF XY: 0.0137 AC XY: 1022AN XY: 74474
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ESP6500AA
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ExAC
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566
Asia WGS
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.
MutationTaster
Benign
N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;.
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