rs376447070
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_001042492.3(NF1):c.960T>A(p.Ala320=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000954 in 1,614,082 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A320A) has been classified as Likely benign.
Frequency
Consequence
NM_001042492.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NF1 | NM_001042492.3 | c.960T>A | p.Ala320= | synonymous_variant | 9/58 | ENST00000358273.9 | |
NF1 | NM_000267.3 | c.960T>A | p.Ala320= | synonymous_variant | 9/57 | ||
NF1 | NM_001128147.3 | c.960T>A | p.Ala320= | synonymous_variant | 9/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NF1 | ENST00000358273.9 | c.960T>A | p.Ala320= | synonymous_variant | 9/58 | 1 | NM_001042492.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 152248Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000183 AC: 46AN: 251422Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135892
GnomAD4 exome AF: 0.0000937 AC: 137AN: 1461834Hom.: 0 Cov.: 31 AF XY: 0.0000853 AC XY: 62AN XY: 727222
GnomAD4 genome ? AF: 0.000112 AC: 17AN: 152248Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74388
ClinVar
Submissions by phenotype
Neurofibromatosis, type 1 Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Mar 15, 2022 | - - |
Hereditary cancer-predisposing syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 18, 2014 | This alteration is classified as likely benign based on a combination of the following: 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at