chrX-64224365-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_130388.4(ASB12):c.927G>A(p.Met309Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000108 in 1,209,151 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 30 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_130388.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ASB12 | NM_130388.4 | c.927G>A | p.Met309Ile | missense_variant | Exon 3 of 3 | ENST00000362002.3 | NP_569059.3 | |
LOC112268307 | XM_047442705.1 | c.125+17325C>T | intron_variant | Intron 2 of 4 | XP_047298661.1 | |||
LOC112268307 | XM_047442706.1 | c.125+17325C>T | intron_variant | Intron 2 of 3 | XP_047298662.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000664 AC: 74AN: 111382Hom.: 0 Cov.: 23 AF XY: 0.000536 AC XY: 18AN XY: 33570
GnomAD3 exomes AF: 0.000114 AC: 21AN: 183412Hom.: 0 AF XY: 0.0000737 AC XY: 5AN XY: 67852
GnomAD4 exome AF: 0.0000519 AC: 57AN: 1097715Hom.: 0 Cov.: 30 AF XY: 0.0000331 AC XY: 12AN XY: 363079
GnomAD4 genome AF: 0.000664 AC: 74AN: 111436Hom.: 0 Cov.: 23 AF XY: 0.000535 AC XY: 18AN XY: 33634
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.927G>A (p.M309I) alteration is located in exon 3 (coding exon 2) of the ASB12 gene. This alteration results from a G to A substitution at nucleotide position 927, causing the methionine (M) at amino acid position 309 to be replaced by an isoleucine (I). 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