rs78661149
Positions:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_001164458.2(ACTR3C):c.361C>T(p.Gln121Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0421 in 148,166 control chromosomes in the GnomAD database, including 205 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.042 ( 205 hom., cov: 30)
Exomes 𝑓: 0.043 ( 2980 hom. )
Failed GnomAD Quality Control
Consequence
ACTR3C
NM_001164458.2 stop_gained
NM_001164458.2 stop_gained
Scores
1
1
5
Clinical Significance
Conservation
PhyloP100: 0.0600
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 7-150286477-G-A is Benign according to our data. Variant chr7-150286477-G-A is described in ClinVar as [Benign]. Clinvar id is 402338.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.072 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACTR3C | NM_001164458.2 | c.361C>T | p.Gln121Ter | stop_gained | 5/8 | ENST00000683684.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACTR3C | ENST00000683684.1 | c.361C>T | p.Gln121Ter | stop_gained | 5/8 | NM_001164458.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0422 AC: 6242AN: 148052Hom.: 203 Cov.: 30
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GnomAD3 exomes AF: 0.0495 AC: 12268AN: 247772Hom.: 478 AF XY: 0.0533 AC XY: 7128AN XY: 133696
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0434 AC: 61001AN: 1406730Hom.: 2980 Cov.: 31 AF XY: 0.0455 AC XY: 31819AN XY: 699942
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GnomAD4 genome ? AF: 0.0421 AC: 6244AN: 148166Hom.: 205 Cov.: 30 AF XY: 0.0430 AC XY: 3104AN XY: 72186
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: ExAC frequency - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Benign
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MutationTaster
Benign
A;A
Vest4
0.24, 0.23
GERP RS
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