10-113854966-CAGG-C
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Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PM4_Supporting
The NM_198514.4(NHLRC2):c.97_99del(p.Glu33del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000285 in 1,401,570 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000029 ( 0 hom. )
Consequence
NHLRC2
NM_198514.4 inframe_deletion
NM_198514.4 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 8.56
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_198514.4. Strenght limited to Supporting due to length of the change: 1aa.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NHLRC2 | NM_198514.4 | c.97_99del | p.Glu33del | inframe_deletion | 1/11 | ENST00000369301.3 | |
NHLRC2 | XM_011539769.4 | c.97_99del | p.Glu33del | inframe_deletion | 1/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NHLRC2 | ENST00000369301.3 | c.97_99del | p.Glu33del | inframe_deletion | 1/11 | 2 | NM_198514.4 | P1 | |
NHLRC2 | ENST00000468890.1 | n.146_148del | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000285 AC: 4AN: 1401570Hom.: 0 AF XY: 0.00000289 AC XY: 2AN XY: 691598
GnomAD4 exome
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GnomAD4 genome Cov.: 32
GnomAD4 genome
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32
Bravo
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Fibrosis, neurodegeneration, and cerebral angiomatosis Uncertain:1
Uncertain significance, criteria provided, single submitter | research | Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin | - | - - |
Computational scores
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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