chr10-113855020-C-T
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_198514.4(NHLRC2):c.148C>T(p.Gln50Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000286 in 1,400,614 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_198514.4 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NHLRC2 | NM_198514.4 | c.148C>T | p.Gln50Ter | stop_gained | 1/11 | ENST00000369301.3 | |
NHLRC2 | XM_011539769.4 | c.148C>T | p.Gln50Ter | stop_gained | 1/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NHLRC2 | ENST00000369301.3 | c.148C>T | p.Gln50Ter | stop_gained | 1/11 | 2 | NM_198514.4 | P1 | |
NHLRC2 | ENST00000468890.1 | n.197C>T | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000632 AC: 1AN: 158196Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 83258
GnomAD4 exome AF: 0.00000286 AC: 4AN: 1400614Hom.: 0 Cov.: 31 AF XY: 0.00000289 AC XY: 2AN XY: 690950
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Fibrosis, neurodegeneration, and cerebral angiomatosis Pathogenic:2
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 20, 2023 | - - |
Pathogenic, criteria provided, single submitter | research | Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin | - | - - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden | Nov 03, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at