chr9-116425856-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001365068.1(ASTN2):c.4015C>T(p.Arg1339Trp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,608,108 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R1339Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001365068.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ASTN2 | NM_001365068.1 | c.4015C>T | p.Arg1339Trp | missense_variant | 23/23 | ENST00000313400.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASTN2 | ENST00000313400.9 | c.4015C>T | p.Arg1339Trp | missense_variant | 23/23 | 5 | NM_001365068.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151640Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251172Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135750
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1456468Hom.: 0 Cov.: 35 AF XY: 0.0000166 AC XY: 12AN XY: 724546
GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151640Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74020
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 22, 2021 | The c.3862C>T (p.R1288W) alteration is located in exon 22 (coding exon 22) of the ASTN2 gene. This alteration results from a C to T substitution at nucleotide position 3862, causing the arginine (R) at amino acid position 1288 to be replaced by a tryptophan (W). 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