chr9-116487369-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001365068.1(ASTN2):c.3487G>A(p.Gly1163Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000105 in 1,613,742 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001365068.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ASTN2 | NM_001365068.1 | c.3487G>A | p.Gly1163Ser | missense_variant | Exon 20 of 23 | ENST00000313400.9 | NP_001351997.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152118Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000478 AC: 12AN: 251060Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135652
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461624Hom.: 0 Cov.: 30 AF XY: 0.00000963 AC XY: 7AN XY: 727110
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152118Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74308
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3334G>A (p.G1112S) alteration is located in exon 19 (coding exon 19) of the ASTN2 gene. This alteration results from a G to A substitution at nucleotide position 3334, causing the glycine (G) at amino acid position 1112 to be replaced by a serine (S). 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