chr16-81315131-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_022041.4(GAN):c.18C>T(p.Ala6=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000365 in 1,370,946 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. AV6A?) has been classified as Pathogenic.
Frequency
Consequence
NM_022041.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GAN | NM_022041.4 | c.18C>T | p.Ala6= | synonymous_variant | 1/11 | ENST00000648994.2 | |
GAN | NM_001377486.1 | c.-507C>T | 5_prime_UTR_variant | 1/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GAN | ENST00000648994.2 | c.18C>T | p.Ala6= | synonymous_variant | 1/11 | NM_022041.4 | P1 | ||
GAN | ENST00000674788.1 | n.143C>T | non_coding_transcript_exon_variant | 1/3 | |||||
GAN | ENST00000648349.2 | c.18C>T | p.Ala6= | synonymous_variant, NMD_transcript_variant | 1/10 | ||||
GAN | ENST00000650388.1 | c.18C>T | p.Ala6= | synonymous_variant, NMD_transcript_variant | 1/9 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 0.00000365 AC: 5AN: 1370946Hom.: 0 Cov.: 32 AF XY: 0.00000443 AC XY: 3AN XY: 677638
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Giant axonal neuropathy 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 21, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.