chr16-81377309-T-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_022041.4(GAN):āc.1593T>Gā(p.Val531=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000233 in 1,599,968 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. V531V) has been classified as Likely benign.
Frequency
Consequence
NM_022041.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GAN | NM_022041.4 | c.1593T>G | p.Val531= | synonymous_variant | 10/11 | ENST00000648994.2 | |
GAN | NM_001377486.1 | c.954T>G | p.Val318= | synonymous_variant | 9/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GAN | ENST00000648994.2 | c.1593T>G | p.Val531= | synonymous_variant | 10/11 | NM_022041.4 | P1 | ||
GAN | ENST00000648349.2 | c.*1301T>G | 3_prime_UTR_variant, NMD_transcript_variant | 9/10 | |||||
GAN | ENST00000650388.1 | c.*950T>G | 3_prime_UTR_variant, NMD_transcript_variant | 8/9 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152226Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000875 AC: 22AN: 251492Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135918
GnomAD4 exome AF: 0.000246 AC: 356AN: 1447742Hom.: 0 Cov.: 26 AF XY: 0.000259 AC XY: 187AN XY: 721302
GnomAD4 genome AF: 0.000105 AC: 16AN: 152226Hom.: 0 Cov.: 32 AF XY: 0.0000941 AC XY: 7AN XY: 74364
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 11, 2019 | 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. - |
Giant axonal neuropathy 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at