chrX-150470447-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_005491.5(MAMLD1):c.874G>A(p.Ala292Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,210,407 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 9 hemizygotes in GnomAD. 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 Likely benign (★★).
Frequency
Consequence
NM_005491.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAMLD1 | NM_005491.5 | c.874G>A | p.Ala292Thr | missense_variant | 4/8 | ENST00000370401.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAMLD1 | ENST00000370401.7 | c.874G>A | p.Ala292Thr | missense_variant | 4/8 | 5 | NM_005491.5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000446 AC: 5AN: 112184Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34366
GnomAD3 exomes AF: 0.0000274 AC: 5AN: 182489Hom.: 0 AF XY: 0.0000298 AC XY: 2AN XY: 67215
GnomAD4 exome AF: 0.0000200 AC: 22AN: 1098170Hom.: 0 Cov.: 34 AF XY: 0.0000248 AC XY: 9AN XY: 363534
GnomAD4 genome ? AF: 0.0000445 AC: 5AN: 112237Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34429
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2024 | MAMLD1: BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at