rs267608339
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 1P and 12B. PM4_SupportingBP6_Very_StrongBS2
The NM_001110792.2(MECP2):βc.1197_1199delβ(p.Pro403del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000128 in 705,455 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (β β ). Synonymous variant affecting the same amino acid position (i.e. P399P) has been classified as Benign.
Frequency
Consequence
NM_001110792.2 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MECP2 | NM_001110792.2 | c.1197_1199del | p.Pro403del | inframe_deletion | 3/3 | ENST00000453960.7 | |
MECP2 | NM_004992.4 | c.1161_1163del | p.Pro391del | inframe_deletion | 4/4 | ENST00000303391.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MECP2 | ENST00000303391.11 | c.1161_1163del | p.Pro391del | inframe_deletion | 4/4 | 1 | NM_004992.4 | P1 | |
MECP2 | ENST00000453960.7 | c.1197_1199del | p.Pro403del | inframe_deletion | 3/3 | 1 | NM_001110792.2 | ||
MECP2 | ENST00000407218.5 | c.*533_*535del | 3_prime_UTR_variant | 4/4 | 5 | ||||
MECP2 | ENST00000628176.2 | c.*533_*535del | 3_prime_UTR_variant | 5/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000935 AC: 2AN: 21381Hom.: 0 Cov.: 20 AF XY: 0.00 AC XY: 0AN XY: 5863
GnomAD3 exomes AF: 0.0000150 AC: 2AN: 133195Hom.: 0 AF XY: 0.0000206 AC XY: 1AN XY: 48655
GnomAD4 exome AF: 0.0000102 AC: 7AN: 684074Hom.: 0 AF XY: 0.0000148 AC XY: 3AN XY: 202488
GnomAD4 genome ? AF: 0.0000935 AC: 2AN: 21381Hom.: 0 Cov.: 20 AF XY: 0.00 AC XY: 0AN XY: 5863
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 15, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Severe neonatal-onset encephalopathy with microcephaly Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 10, 2023 | - - |
not provided Other:1
not provided, no classification provided | literature only | RettBASE | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at