rs146576740
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_022041.4(GAN):c.1445C>A(p.Ala482Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A482V) has been classified as Likely benign.
Frequency
Consequence
NM_022041.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GAN | NM_022041.4 | c.1445C>A | p.Ala482Asp | missense_variant | 9/11 | ENST00000648994.2 | |
GAN | NM_001377486.1 | c.806C>A | p.Ala269Asp | missense_variant | 8/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GAN | ENST00000648994.2 | c.1445C>A | p.Ala482Asp | missense_variant | 9/11 | NM_022041.4 | P1 | ||
GAN | ENST00000567335.1 | n.3C>A | non_coding_transcript_exon_variant | 1/2 | 3 | ||||
GAN | ENST00000648349.2 | c.*1153C>A | 3_prime_UTR_variant, NMD_transcript_variant | 8/10 | |||||
GAN | ENST00000650388.1 | c.*802C>A | 3_prime_UTR_variant, NMD_transcript_variant | 7/9 |
Frequencies
GnomAD3 genomes ? Cov.: 30
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251492Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135922
GnomAD4 exome Cov.: 32
GnomAD4 genome ? Cov.: 30
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at