chr5-151117173-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001155.5(ANXA6):c.1526G>A(p.Arg509His) variant causes a missense change. The variant allele was found at a frequency of 0.000049 in 1,591,298 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. R509C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001155.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANXA6 | NM_001155.5 | c.1526G>A | p.Arg509His | missense_variant | 20/26 | ENST00000354546.10 | |
ANXA6 | NM_001363114.2 | c.1526G>A | p.Arg509His | missense_variant | 20/25 | ||
ANXA6 | NM_001193544.2 | c.1430G>A | p.Arg477His | missense_variant | 19/25 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANXA6 | ENST00000354546.10 | c.1526G>A | p.Arg509His | missense_variant | 20/26 | 1 | NM_001155.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000427 AC: 1AN: 234042Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 127352
GnomAD4 exome AF: 0.0000507 AC: 73AN: 1439158Hom.: 0 Cov.: 31 AF XY: 0.0000489 AC XY: 35AN XY: 715048
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152140Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74310
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 22, 2023 | The c.1526G>A (p.R509H) alteration is located in exon 20 (coding exon 19) of the ANXA6 gene. This alteration results from a G to A substitution at nucleotide position 1526, causing the arginine (R) at amino acid position 509 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at