17-56594262-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_005450.6(NOG):c.39C>A(p.Ala13=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000275 in 1,457,128 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. A13A) has been classified as Likely benign.
Frequency
Consequence
NM_005450.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NOG | NM_005450.6 | c.39C>A | p.Ala13= | synonymous_variant | 1/1 | ENST00000332822.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOG | ENST00000332822.6 | c.39C>A | p.Ala13= | synonymous_variant | 1/1 | NM_005450.6 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.0000175 AC: 4AN: 227922Hom.: 0 AF XY: 0.00000797 AC XY: 1AN XY: 125464
GnomAD4 exome AF: 0.00000275 AC: 4AN: 1457128Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 724686
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 03, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at