chr6-108868953-C-T
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_032131.6(ARMC2):c.421C>T(p.Gln141Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Consequence
ARMC2
NM_032131.6 stop_gained
NM_032131.6 stop_gained
Scores
4
1
2
Clinical Significance
Conservation
PhyloP100: 1.54
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 11 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 6-108868953-C-T is Pathogenic according to our data. Variant chr6-108868953-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 627631.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-108868953-C-T is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARMC2 | NM_032131.6 | c.421C>T | p.Gln141Ter | stop_gained | 4/18 | ENST00000392644.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARMC2 | ENST00000392644.9 | c.421C>T | p.Gln141Ter | stop_gained | 4/18 | 1 | NM_032131.6 | P1 | |
ARMC2 | ENST00000237512.4 | c.421C>T | p.Gln141Ter | stop_gained | 4/5 | 2 | |||
ARMC2 | ENST00000368972.7 | c.-75C>T | 5_prime_UTR_variant | 3/17 | 2 | ||||
ARMC2 | ENST00000414610.1 | upstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Spermatogenic failure 38 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | May 15, 2019 | - - |
Male infertility with teratozoospermia due to single gene mutation Pathogenic:1
Pathogenic, no assertion criteria provided | case-control | Genetics of Infertility and Preimplantation Genetic Diagnosis, Centre Hospitalier Universitaire Grenoble Alpes | Dec 17, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Benign
D
MutationTaster
Benign
A;D
Vest4
GERP RS
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at