7-143756089-C-A
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_StrongBP6_Moderate
The NM_178561.5(CTAGE6):c.1570G>T(p.Ala524Ser) 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.00039 ( 0 hom., cov: 9)
Exomes 𝑓: 0.00096 ( 45 hom. )
Failed GnomAD Quality Control
Consequence
CTAGE6
NM_178561.5 missense
NM_178561.5 missense
Scores
1
10
Clinical Significance
Conservation
PhyloP100: 0.965
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 -5 ACMG points.
PP2
Missense variant where missense usually causes diseases, CTAGE6
BP4
Computational evidence support a benign effect (MetaRNN=0.00538826).
BP6
Variant 7-143756089-C-A is Benign according to our data. Variant chr7-143756089-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2658120.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTAGE6 | NM_178561.5 | c.1570G>T | p.Ala524Ser | missense_variant | 1/1 | ENST00000470691.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTAGE6 | ENST00000470691.2 | c.1570G>T | p.Ala524Ser | missense_variant | 1/1 | NM_178561.5 | P1 | ||
ENST00000700950.1 | n.178+13009G>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 30AN: 77308Hom.: 0 Cov.: 9 FAILED QC
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GnomAD3 exomes AF: 0.000817 AC: 54AN: 66094Hom.: 3 AF XY: 0.000982 AC XY: 33AN XY: 33612
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000964 AC: 1000AN: 1037796Hom.: 45 Cov.: 17 AF XY: 0.00120 AC XY: 617AN XY: 514880
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000388 AC: 30AN: 77380Hom.: 0 Cov.: 9 AF XY: 0.000285 AC XY: 10AN XY: 35100
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2024 | CTAGE6: PP2, BP4, BS2 - |
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
D
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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at