rs200977419
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_002473.6(MYH9):c.4344+10C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000625 in 1,614,094 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_002473.6 intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYH9 | NM_002473.6 | c.4344+10C>T | intron_variant | Intron 31 of 40 | ENST00000216181.11 | NP_002464.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYH9 | ENST00000216181.11 | c.4344+10C>T | intron_variant | Intron 31 of 40 | 1 | NM_002473.6 | ENSP00000216181.6 | |||
MYH9 | ENST00000685801.1 | c.4407+10C>T | intron_variant | Intron 32 of 41 | ENSP00000510688.1 | |||||
MYH9 | ENST00000691109.1 | n.4639+10C>T | intron_variant | Intron 25 of 34 |
Frequencies
GnomAD3 genomes AF: 0.000611 AC: 93AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000451 AC: 113AN: 250710Hom.: 0 AF XY: 0.000494 AC XY: 67AN XY: 135600
GnomAD4 exome AF: 0.000627 AC: 916AN: 1461776Hom.: 0 Cov.: 32 AF XY: 0.000613 AC XY: 446AN XY: 727194
GnomAD4 genome AF: 0.000611 AC: 93AN: 152318Hom.: 0 Cov.: 33 AF XY: 0.000510 AC XY: 38AN XY: 74466
ClinVar
Submissions by phenotype
not specified Benign:3
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. -
c.4344+10C>T in intron 31 of MYH9: This variant is not expected to have clinical significance because it is not located within the conserved splice consensus se quence and has been identified in 95/126020 of European chromosomes by the Genom e Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs200977 419). -
- -
not provided Benign:2
- -
- -
Autosomal dominant nonsyndromic hearing loss 17 Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
Autosomal dominant nonsyndromic hearing loss 17;C5200934:Macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss Benign:1
- -
MYH9-related disorder Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at