chrX-150470432-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_005491.5(MAMLD1):c.859G>A(p.Ala287Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000719 in 1,210,464 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. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_005491.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAMLD1 | NM_005491.5 | c.859G>A | p.Ala287Thr | missense_variant | 4/8 | ENST00000370401.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAMLD1 | ENST00000370401.7 | c.859G>A | p.Ala287Thr | missense_variant | 4/8 | 5 | NM_005491.5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000801 AC: 9AN: 112311Hom.: 0 Cov.: 23 AF XY: 0.0000580 AC XY: 2AN XY: 34467
GnomAD3 exomes AF: 0.0000329 AC: 6AN: 182499Hom.: 0 AF XY: 0.0000298 AC XY: 2AN XY: 67199
GnomAD4 exome AF: 0.0000710 AC: 78AN: 1098153Hom.: 0 Cov.: 34 AF XY: 0.0000770 AC XY: 28AN XY: 363513
GnomAD4 genome ? AF: 0.0000801 AC: 9AN: 112311Hom.: 0 Cov.: 23 AF XY: 0.0000580 AC XY: 2AN XY: 34467
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 28, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at