7-143756800-T-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP2BP4_Strong
The NM_178561.5(CTAGE6):c.859A>G(p.Thr287Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 10/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0000070 ( 0 hom., cov: 23)
Exomes 𝑓: 0.000016 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CTAGE6
NM_178561.5 missense
NM_178561.5 missense
Scores
1
10
Clinical Significance
Conservation
PhyloP100: -0.633
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=0.04364863).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTAGE6 | NM_178561.5 | c.859A>G | p.Thr287Ala | missense_variant | 1/1 | ENST00000470691.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTAGE6 | ENST00000470691.2 | c.859A>G | p.Thr287Ala | missense_variant | 1/1 | NM_178561.5 | P1 | ||
ENST00000700950.1 | n.178+12298A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00000697 AC: 1AN: 143390Hom.: 0 Cov.: 23
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000159 AC: 22AN: 1387756Hom.: 0 Cov.: 31 AF XY: 0.0000175 AC XY: 12AN XY: 686386
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.00000697 AC: 1AN: 143390Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 69636
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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 | Jan 09, 2024 | The c.859A>G (p.T287A) alteration is located in exon 1 (coding exon 1) of the CTAGE6 gene. This alteration results from a A to G substitution at nucleotide position 859, causing the threonine (T) at amino acid position 287 to be replaced by an alanine (A). 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
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