chr16-81315126-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_022041.4(GAN):c.13A>C(p.Ser5Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000146 in 1,365,430 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S5N) has been classified as Uncertain significance.
Frequency
Consequence
NM_022041.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GAN | NM_022041.4 | c.13A>C | p.Ser5Arg | missense_variant | 1/11 | ENST00000648994.2 | |
GAN | NM_001377486.1 | c.-512A>C | 5_prime_UTR_variant | 1/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GAN | ENST00000648994.2 | c.13A>C | p.Ser5Arg | missense_variant | 1/11 | NM_022041.4 | P1 | ||
GAN | ENST00000674788.1 | n.138A>C | non_coding_transcript_exon_variant | 1/3 | |||||
GAN | ENST00000648349.2 | c.13A>C | p.Ser5Arg | missense_variant, NMD_transcript_variant | 1/10 | ||||
GAN | ENST00000650388.1 | c.13A>C | p.Ser5Arg | missense_variant, NMD_transcript_variant | 1/9 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 0.00000146 AC: 2AN: 1365430Hom.: 0 Cov.: 32 AF XY: 0.00000148 AC XY: 1AN XY: 674550
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.