rs145446060
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000268.4(NF2):c.1753G>A(p.Ala585Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000942 in 1,613,584 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000268.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NF2 | NM_000268.4 | c.1753G>A | p.Ala585Thr | missense_variant | 16/16 | ENST00000338641.10 | NP_000259.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NF2 | ENST00000338641.10 | c.1753G>A | p.Ala585Thr | missense_variant | 16/16 | 1 | NM_000268.4 | ENSP00000344666 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000381 AC: 58AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000144 AC: 36AN: 249906Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135164
GnomAD4 exome AF: 0.0000636 AC: 93AN: 1461328Hom.: 0 Cov.: 31 AF XY: 0.0000605 AC XY: 44AN XY: 726896
GnomAD4 genome AF: 0.000388 AC: 59AN: 152256Hom.: 0 Cov.: 32 AF XY: 0.000430 AC XY: 32AN XY: 74442
ClinVar
Submissions by phenotype
Neurofibromatosis, type 2 Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 25, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | All of Us Research Program, National Institutes of Health | Feb 05, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Mar 09, 2022 | - - |
Hereditary cancer-predisposing syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 02, 2019 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at