7-143756209-C-G
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP2BP4
The NM_178561.5(CTAGE6):āc.1450G>Cā(p.Ala484Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: not found (cov: 22)
Exomes š: 0.0000049 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CTAGE6
NM_178561.5 missense
NM_178561.5 missense
Scores
1
4
6
Clinical Significance
Conservation
PhyloP100: -0.403
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 Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP2
Missense variant where missense usually causes diseases, CTAGE6
BP4
Computational evidence support a benign effect (MetaRNN=0.2859912).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTAGE6 | NM_178561.5 | c.1450G>C | p.Ala484Pro | missense_variant | 1/1 | ENST00000470691.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTAGE6 | ENST00000470691.2 | c.1450G>C | p.Ala484Pro | missense_variant | 1/1 | NM_178561.5 | P1 | ||
ENST00000700950.1 | n.178+12889G>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD3 genomes
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22
GnomAD3 exomes AF: 0.00000582 AC: 1AN: 171690Hom.: 0 AF XY: 0.0000107 AC XY: 1AN XY: 93438
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000493 AC: 7AN: 1420036Hom.: 0 Cov.: 31 AF XY: 0.00000568 AC XY: 4AN XY: 703828
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome Cov.: 22
GnomAD4 genome
Cov.:
22
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 | Apr 14, 2022 | The c.1450G>C (p.A484P) alteration is located in exon 1 (coding exon 1) of the CTAGE6 gene. This alteration results from a G to C substitution at nucleotide position 1450, causing the alanine (A) at amino acid position 484 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
FATHMM_MKL
Benign
N
M_CAP
Benign
T
MetaRNN
Benign
T
MutationAssessor
Uncertain
M
PrimateAI
Uncertain
T
Sift4G
Uncertain
T
Polyphen
D
Vest4
MVP
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
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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