rs267608636
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2
The NM_001110792.2(MECP2):c.1474C>T(p.Pro492Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000248 in 1,209,666 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P492L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001110792.2 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 |
---|---|---|---|---|---|---|---|
MECP2 | NM_001110792.2 | c.1474C>T | p.Pro492Ser | missense_variant | 3/3 | ENST00000453960.7 | |
MECP2 | NM_004992.4 | c.1438C>T | p.Pro480Ser | missense_variant | 4/4 | ENST00000303391.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MECP2 | ENST00000453960.7 | c.1474C>T | p.Pro492Ser | missense_variant | 3/3 | 1 | NM_001110792.2 | ||
MECP2 | ENST00000303391.11 | c.1438C>T | p.Pro480Ser | missense_variant | 4/4 | 1 | NM_004992.4 | P1 | |
MECP2 | ENST00000628176.2 | c.*810C>T | 3_prime_UTR_variant | 5/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000898 AC: 1AN: 111378Hom.: 0 Cov.: 23 AF XY: 0.0000298 AC XY: 1AN XY: 33546
GnomAD3 exomes AF: 0.0000109 AC: 2AN: 183504Hom.: 0 AF XY: 0.0000294 AC XY: 2AN XY: 67934
GnomAD4 exome AF: 0.00000182 AC: 2AN: 1098236Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 1AN XY: 363592
GnomAD4 genome ? AF: 0.00000897 AC: 1AN: 111430Hom.: 0 Cov.: 23 AF XY: 0.0000298 AC XY: 1AN XY: 33608
ClinVar
Submissions by phenotype
Rett syndrome Benign:1
Benign, criteria provided, single submitter | curation | Centre for Population Genomics, CPG | Mar 14, 2024 | This variant has been collected from RettBASE and curated to current modified ACMG/AMP criteria. Based on the classification scheme defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like Disorders Specifications to the ACMG/AMP Variant Interpretation Guidelines VCEP 3.0, this variant is classified as benign. At least the following criteria are met: The allele frequency of this variant in at least one population in gnomAD is higher than the 0.03% threshold defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like Disorders VCEP 3.0 (BA1). - |
not specified Benign:1
Benign, no assertion criteria provided | curation | RettBASE | May 14, 2010 | - - |
Severe neonatal-onset encephalopathy with microcephaly Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 05, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at