1-197086846-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018136.5(ASPM):c.10288C>T(p.Pro3430Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000664 in 1,611,540 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018136.5 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ASPM | NM_018136.5 | c.10288C>T | p.Pro3430Ser | missense_variant | 27/28 | ENST00000367409.9 | |
ASPM | NM_001206846.2 | c.5533C>T | p.Pro1845Ser | missense_variant | 26/27 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASPM | ENST00000367409.9 | c.10288C>T | p.Pro3430Ser | missense_variant | 27/28 | 1 | NM_018136.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 152064Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250750Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135538
GnomAD4 exome AF: 0.0000692 AC: 101AN: 1459476Hom.: 0 Cov.: 32 AF XY: 0.0000620 AC XY: 45AN XY: 726216
GnomAD4 genome ? AF: 0.0000395 AC: 6AN: 152064Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74276
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 16, 2023 | The c.10288C>T (p.P3430S) alteration is located in exon 27 (coding exon 27) of the ASPM gene. This alteration results from a C to T substitution at nucleotide position 10288, causing the proline (P) at amino acid position 3430 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