20-10412638-A-ACAGG
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_170784.3(MKKS):c.876_877insCCTG(p.Cys293ProfsTer35) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,860 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. L292L) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_170784.3 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MKKS | NM_170784.3 | c.876_877insCCTG | p.Cys293ProfsTer35 | frameshift_variant | 3/6 | ENST00000347364.7 | |
MKKS | NM_018848.3 | c.876_877insCCTG | p.Cys293ProfsTer35 | frameshift_variant | 3/6 | ||
MKKS | NR_072977.2 | n.347-3836_347-3835insCCTG | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MKKS | ENST00000347364.7 | c.876_877insCCTG | p.Cys293ProfsTer35 | frameshift_variant | 3/6 | 1 | NM_170784.3 | P1 | |
MKKS | ENST00000399054.6 | c.876_877insCCTG | p.Cys293ProfsTer35 | frameshift_variant | 3/6 | 1 | P1 | ||
MKKS | ENST00000651692.1 | c.876_877insCCTG | p.Cys293ProfsTer35 | frameshift_variant | 4/7 | P1 | |||
MKKS | ENST00000652676.1 | n.520_521insCCTG | non_coding_transcript_exon_variant | 4/7 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461860Hom.: 0 Cov.: 33 AF XY: 0.00000550 AC XY: 4AN XY: 727232
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Bardet-Biedl syndrome Pathogenic:1
Pathogenic, no assertion criteria provided | curation | GeneReviews | Oct 13, 2009 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at