chrX-150462831-A-G
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_005491.5(MAMLD1):c.156A>G(p.Pro52=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00262 in 1,206,952 control chromosomes in the GnomAD database, including 47 homozygotes. There are 825 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.013 ( 17 hom., 370 hem., cov: 23)
Exomes 𝑓: 0.0016 ( 30 hom. 455 hem. )
Consequence
MAMLD1
NM_005491.5 synonymous
NM_005491.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.138
Genes affected
MAMLD1 (HGNC:2568): (mastermind like domain containing 1) This gene encodes a mastermind-like domain containing protein. This protein may function as a transcriptional co-activator. Mutations in this gene are the cause of X-linked hypospadias type 2. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Apr 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
Variant X-150462831-A-G is Benign according to our data. Variant chrX-150462831-A-G is described in ClinVar as [Benign]. Clinvar id is 714971.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.138 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0129 (1450/112309) while in subpopulation AFR AF= 0.0439 (1354/30874). AF 95% confidence interval is 0.0419. There are 17 homozygotes in gnomad4. There are 370 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 17 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAMLD1 | NM_005491.5 | c.156A>G | p.Pro52= | synonymous_variant | 3/8 | ENST00000370401.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAMLD1 | ENST00000370401.7 | c.156A>G | p.Pro52= | synonymous_variant | 3/8 | 5 | NM_005491.5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0129 AC: 1453AN: 112255Hom.: 17 Cov.: 23 AF XY: 0.0108 AC XY: 371AN XY: 34411
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GnomAD3 exomes AF: 0.00392 AC: 711AN: 181375Hom.: 18 AF XY: 0.00227 AC XY: 153AN XY: 67257
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GnomAD4 exome AF: 0.00156 AC: 1712AN: 1094643Hom.: 30 Cov.: 29 AF XY: 0.00126 AC XY: 455AN XY: 360091
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 25, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at