rs542791128
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_002473.6(MYH9):c.3697G>A(p.Val1233Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000416 in 1,614,126 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_002473.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYH9 | NM_002473.6 | c.3697G>A | p.Val1233Met | missense_variant | 28/41 | ENST00000216181.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYH9 | ENST00000216181.11 | c.3697G>A | p.Val1233Met | missense_variant | 28/41 | 1 | NM_002473.6 | P1 | |
MYH9 | ENST00000685801.1 | c.3760G>A | p.Val1254Met | missense_variant | 29/42 | ||||
MYH9 | ENST00000691109.1 | n.3992G>A | non_coding_transcript_exon_variant | 22/35 |
Frequencies
GnomAD3 genomes ? AF: 0.000289 AC: 44AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000816 AC: 205AN: 251376Hom.: 1 AF XY: 0.00115 AC XY: 156AN XY: 135858
GnomAD4 exome AF: 0.000430 AC: 628AN: 1461808Hom.: 7 Cov.: 35 AF XY: 0.000628 AC XY: 457AN XY: 727194
GnomAD4 genome ? AF: 0.000289 AC: 44AN: 152318Hom.: 0 Cov.: 33 AF XY: 0.000430 AC XY: 32AN XY: 74492
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 12, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 29, 2021 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jun 26, 2017 | p.Val1233Met variant in exon 28 of MYH9: This variant is not expected to have cl inical significance because it has been identified in 0.6% (179/30782) of South Asian chromosomes including 1 homozygote in the Genome Aggregation Database (gno mAD, http://gnomad.broadinstitute.org; dbSNP rs542791128), and in 2.9% (6/206) o f GIH Indian chromosomes by the 1000 Genomes Project. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at