1-176888072-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004319.3(ASTN1):c.3073G>C(p.Val1025Leu) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004319.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ASTN1 | NM_004319.3 | c.3073G>C | p.Val1025Leu | missense_variant, splice_region_variant | 18/23 | ENST00000361833.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASTN1 | ENST00000361833.7 | c.3073G>C | p.Val1025Leu | missense_variant, splice_region_variant | 18/23 | 1 | NM_004319.3 | P1 | |
ASTN1 | ENST00000367657.7 | c.3073G>C | p.Val1025Leu | missense_variant, splice_region_variant | 18/23 | 1 | |||
ASTN1 | ENST00000424564.2 | c.3073G>C | p.Val1025Leu | missense_variant, splice_region_variant | 18/22 | 1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 29
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2022 | The c.3073G>C (p.V1025L) alteration is located in exon 18 (coding exon 18) of the ASTN1 gene. This alteration results from a G to C substitution at nucleotide position 3073, causing the valine (V) at amino acid position 1025 to be replaced by a leucine (L). 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