17-2081926-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_017575.5(SMG6):c.3565G>A(p.Glu1189Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00344 in 1,614,170 control chromosomes in the GnomAD database, including 172 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Genomes: 𝑓 0.018 ( 92 hom., cov: 32)
Exomes 𝑓: 0.0019 ( 80 hom. )
Consequence
SMG6
NM_017575.5 missense
NM_017575.5 missense
Scores
1
5
12
Clinical Significance
Conservation
PhyloP100: 6.87
Genes affected
SMG6 (HGNC:17809): (SMG6 nonsense mediated mRNA decay factor) This gene encodes a component of the telomerase ribonucleoprotein complex responsible for the replication and maintenance of chromosome ends. The encoded protein also plays a role in the nonsense-mediated mRNA decay (NMD) pathway, providing the endonuclease activity near the premature translation termination codon that is needed to initiate NMD. Alternatively spliced transcript variants encoding distinct protein isoforms have been described. [provided by RefSeq, Feb 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0022273958).
BP6
?
Variant 17-2081926-C-T is Benign according to our data. Variant chr17-2081926-C-T is described in ClinVar as [Benign]. Clinvar id is 789651.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0618 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMG6 | NM_017575.5 | c.3565G>A | p.Glu1189Lys | missense_variant | 15/19 | ENST00000263073.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMG6 | ENST00000263073.11 | c.3565G>A | p.Glu1189Lys | missense_variant | 15/19 | 1 | NM_017575.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0182 AC: 2773AN: 152210Hom.: 92 Cov.: 32
GnomAD3 genomes
?
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2773
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GnomAD3 exomes AF: 0.00453 AC: 1139AN: 251382Hom.: 40 AF XY: 0.00344 AC XY: 468AN XY: 135864
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GnomAD4 exome AF: 0.00190 AC: 2781AN: 1461842Hom.: 80 Cov.: 32 AF XY: 0.00163 AC XY: 1183AN XY: 727224
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GnomAD4 genome ? AF: 0.0182 AC: 2775AN: 152328Hom.: 92 Cov.: 32 AF XY: 0.0177 AC XY: 1315AN XY: 74490
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?
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ESP6500AA
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285
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ExAC
?
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697
Asia WGS
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17
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3478
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 08, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T;.;.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;.;D;D
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;.;.
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;.;N;.
REVEL
Benign
Sift
Benign
T;.;D;.
Sift4G
Benign
T;T;T;T
Polyphen
P;.;.;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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