rs113698937
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_002473.6(MYH9):c.3838-12C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00307 in 1,609,590 control chromosomes in the GnomAD database, including 99 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_002473.6 intron
Scores
Clinical Significance
Conservation
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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.3838-12C>T | intron_variant | Intron 28 of 40 | ENST00000216181.11 | NP_002464.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYH9 | ENST00000216181.11 | c.3838-12C>T | intron_variant | Intron 28 of 40 | 1 | NM_002473.6 | ENSP00000216181.6 | |||
MYH9 | ENST00000685801.1 | c.3901-12C>T | intron_variant | Intron 29 of 41 | ENSP00000510688.1 | |||||
MYH9 | ENST00000691109.1 | n.4133-12C>T | intron_variant | Intron 22 of 34 |
Frequencies
GnomAD3 genomes AF: 0.0141 AC: 2143AN: 152076Hom.: 54 Cov.: 32
GnomAD3 exomes AF: 0.00450 AC: 1093AN: 242704Hom.: 18 AF XY: 0.00344 AC XY: 452AN XY: 131560
GnomAD4 exome AF: 0.00192 AC: 2796AN: 1457396Hom.: 45 Cov.: 32 AF XY: 0.00170 AC XY: 1235AN XY: 724826
GnomAD4 genome AF: 0.0141 AC: 2146AN: 152194Hom.: 54 Cov.: 32 AF XY: 0.0134 AC XY: 995AN XY: 74400
ClinVar
Submissions by phenotype
not provided Benign:5
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not specified Benign:3
3838-12C>T in Intron 28 of MYH9: This variant is not expected to have clinical s ignificance because it has been identified in 3.9% (145/3736) of African America n chromosomes from a broad population by the NHLBI Exome Sequencing Project (htt p://evs.gs.washington.edu/EVS; dbSNP rs113698937). -
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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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
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