chr7-143755842-T-C
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_StrongBP6_ModerateBS1BS2
The NM_178561.5(CTAGE6):āc.1817A>Gā(p.Lys606Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 11/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.0 ( 0 hom., cov: 0)
Exomes š: 0.0038 ( 3 hom. )
Failed GnomAD Quality Control
Consequence
CTAGE6
NM_178561.5 missense
NM_178561.5 missense
Scores
11
Clinical Significance
Conservation
PhyloP100: 0.565
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 Benign. Variant got -13 ACMG points.
PP2
Missense variant where missense usually causes diseases, CTAGE6
BP4
Computational evidence support a benign effect (MetaRNN=0.004891008).
BP6
Variant 7-143755842-T-C is Benign according to our data. Variant chr7-143755842-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2230027.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population sas. gnomad4_exome allele frequency = 0.00378 (705/186590) while in subpopulation SAS AF= 0.0216 (417/19268). AF 95% confidence interval is 0.0199. There are 3 homozygotes in gnomad4_exome. There are 481 alleles in male gnomad4_exome subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTAGE6 | NM_178561.5 | c.1817A>G | p.Lys606Arg | missense_variant | 1/1 | ENST00000470691.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTAGE6 | ENST00000470691.2 | c.1817A>G | p.Lys606Arg | missense_variant | 1/1 | NM_178561.5 | P1 | ||
ENST00000700950.1 | n.178+13256A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 26Hom.: 0 Cov.: 0 FAILED QC
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GnomAD3 exomes AF: 0.00551 AC: 131AN: 23788Hom.: 2 AF XY: 0.00623 AC XY: 78AN XY: 12530
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GnomAD4 exome AF: 0.00378 AC: 705AN: 186590Hom.: 3 Cov.: 0 AF XY: 0.00496 AC XY: 481AN XY: 97044
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GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 28Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 6
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Data not reliable, filtered out with message: AC0;AS_VQSR
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 25, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
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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
Benign
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