9-116487411-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001365068.1(ASTN2):c.3445G>A(p.Val1149Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00343 in 1,614,014 control chromosomes in the GnomAD database, including 166 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001365068.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ASTN2 | NM_001365068.1 | c.3445G>A | p.Val1149Ile | missense_variant | 20/23 | ENST00000313400.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASTN2 | ENST00000313400.9 | c.3445G>A | p.Val1149Ile | missense_variant | 20/23 | 5 | NM_001365068.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0182 AC: 2773AN: 152098Hom.: 89 Cov.: 32
GnomAD3 exomes AF: 0.00479 AC: 1204AN: 251332Hom.: 28 AF XY: 0.00348 AC XY: 472AN XY: 135816
GnomAD4 exome AF: 0.00189 AC: 2760AN: 1461798Hom.: 76 Cov.: 30 AF XY: 0.00162 AC XY: 1178AN XY: 727206
GnomAD4 genome ? AF: 0.0183 AC: 2782AN: 152216Hom.: 90 Cov.: 32 AF XY: 0.0176 AC XY: 1311AN XY: 74424
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at