chr17-31095315-C-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_Very_StrongBP7BS2_Supporting
The NM_001042492.3(NF1):āc.6C>Gā(p.Ala2=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000938 in 1,385,670 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 (ā ā ). Synonymous variant affecting the same amino acid position (i.e. A2A) 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 -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NF1 | NM_001042492.3 | c.6C>G | p.Ala2= | synonymous_variant | 1/58 | ENST00000358273.9 | |
NF1 | NM_000267.3 | c.6C>G | p.Ala2= | synonymous_variant | 1/57 | ||
NF1 | NM_001128147.3 | c.6C>G | p.Ala2= | synonymous_variant | 1/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NF1 | ENST00000358273.9 | c.6C>G | p.Ala2= | synonymous_variant | 1/58 | 1 | NM_001042492.3 | P1 | |
MIR4733HG | ENST00000583377.1 | n.136G>C | non_coding_transcript_exon_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD3 exomes AF: 0.0000150 AC: 2AN: 133584Hom.: 0 AF XY: 0.0000138 AC XY: 1AN XY: 72712
GnomAD4 exome AF: 0.00000938 AC: 13AN: 1385670Hom.: 0 Cov.: 33 AF XY: 0.0000146 AC XY: 10AN XY: 683628
GnomAD4 genome Cov.: 30
ClinVar
Submissions by phenotype
Neurofibromatosis, type 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 06, 2022 | - - |
Hereditary cancer-predisposing syndrome;CN230736:Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 25, 2021 | 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at