chr7-143756073-C-T
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP2BP4_Strong
The NM_178561.5(CTAGE6):c.1586G>A(p.Arg529His) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 10/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00019 ( 0 hom., cov: 8)
Exomes 𝑓: 0.000032 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CTAGE6
NM_178561.5 missense
NM_178561.5 missense
Scores
1
10
Clinical Significance
Conservation
PhyloP100: 1.21
Genes affected
CTAGE6 (HGNC:28644): (CTAGE family member 6) Predicted to be involved in endoplasmic reticulum to Golgi vesicle-mediated transport; protein secretion; and vesicle cargo loading. Predicted to be integral component of membrane. Predicted to be active in endoplasmic reticulum exit site and endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PP2
Missense variant where missense usually causes diseases, CTAGE6
BP4
Computational evidence support a benign effect (MetaRNN=0.04818356).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTAGE6 | NM_178561.5 | c.1586G>A | p.Arg529His | missense_variant | 1/1 | ENST00000470691.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTAGE6 | ENST00000470691.2 | c.1586G>A | p.Arg529His | missense_variant | 1/1 | NM_178561.5 | P1 | ||
ENST00000700950.1 | n.178+13025G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 13AN: 67228Hom.: 0 Cov.: 8 FAILED QC
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GnomAD3 exomes AF: 0.0000488 AC: 3AN: 61536Hom.: 0 AF XY: 0.0000962 AC XY: 3AN XY: 31188
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000321 AC: 31AN: 965350Hom.: 0 Cov.: 15 AF XY: 0.0000313 AC XY: 15AN XY: 479904
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000193 AC: 13AN: 67284Hom.: 0 Cov.: 8 AF XY: 0.0000993 AC XY: 3AN XY: 30218
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 29, 2022 | The c.1586G>A (p.R529H) alteration is located in exon 1 (coding exon 1) of the CTAGE6 gene. This alteration results from a G to A substitution at nucleotide position 1586, causing the arginine (R) at amino acid position 529 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
FATHMM_MKL
Benign
N
M_CAP
Benign
T
MetaRNN
Benign
T
MutationAssessor
Benign
N
PrimateAI
Uncertain
T
Sift4G
Benign
T
Polyphen
B
Vest4
MVP
GERP RS
Varity_R
gMVP
Splicing
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Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at