chrX-150470648-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005491.5(MAMLD1):c.1075C>T(p.Pro359Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 1,209,970 control chromosomes in the GnomAD database, including 5,619 homozygotes. There are 42,894 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_005491.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAMLD1 | NM_005491.5 | c.1075C>T | p.Pro359Ser | missense_variant | 4/8 | ENST00000370401.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAMLD1 | ENST00000370401.7 | c.1075C>T | p.Pro359Ser | missense_variant | 4/8 | 5 | NM_005491.5 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0825 AC: 9227AN: 111791Hom.: 408 Cov.: 23 AF XY: 0.0751 AC XY: 2550AN XY: 33969
GnomAD3 exomes AF: 0.0829 AC: 15030AN: 181336Hom.: 506 AF XY: 0.0851 AC XY: 5691AN XY: 66858
GnomAD4 exome AF: 0.113 AC: 123680AN: 1098127Hom.: 5211 Cov.: 35 AF XY: 0.111 AC XY: 40344AN XY: 363487
GnomAD4 genome AF: 0.0825 AC: 9222AN: 111843Hom.: 408 Cov.: 23 AF XY: 0.0749 AC XY: 2550AN XY: 34031
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at