X-64224995-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_130388.4(ASB12):c.656G>A(p.Arg219His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000474 in 1,203,311 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 18 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R219C) has been classified as Uncertain significance.
Frequency
Consequence
NM_130388.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ASB12 | NM_130388.4 | c.656G>A | p.Arg219His | missense_variant | Exon 2 of 3 | ENST00000362002.3 | NP_569059.3 | |
LOC112268307 | XM_047442705.1 | c.125+17955C>T | intron_variant | Intron 2 of 4 | XP_047298661.1 | |||
LOC112268307 | XM_047442706.1 | c.125+17955C>T | intron_variant | Intron 2 of 3 | XP_047298662.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000804 AC: 9AN: 111975Hom.: 0 Cov.: 22 AF XY: 0.0000879 AC XY: 3AN XY: 34149
GnomAD3 exomes AF: 0.0000527 AC: 9AN: 170890Hom.: 0 AF XY: 0.0000327 AC XY: 2AN XY: 61138
GnomAD4 exome AF: 0.0000440 AC: 48AN: 1091336Hom.: 0 Cov.: 32 AF XY: 0.0000417 AC XY: 15AN XY: 359438
GnomAD4 genome AF: 0.0000804 AC: 9AN: 111975Hom.: 0 Cov.: 22 AF XY: 0.0000879 AC XY: 3AN XY: 34149
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.656G>A (p.R219H) alteration is located in exon 2 (coding exon 1) of the ASB12 gene. This alteration results from a G to A substitution at nucleotide position 656, causing the arginine (R) at amino acid position 219 to be replaced by a histidine (H). 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