chr22-36293825-G-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_002473.6(MYH9):c.3876C>T(p.Ser1292=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000471 in 1,613,798 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 (★★). Synonymous variant affecting the same amino acid position (i.e. S1292S) has been classified as Likely benign.
Frequency
Consequence
NM_002473.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYH9 | NM_002473.6 | c.3876C>T | p.Ser1292= | synonymous_variant | 29/41 | ENST00000216181.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYH9 | ENST00000216181.11 | c.3876C>T | p.Ser1292= | synonymous_variant | 29/41 | 1 | NM_002473.6 | P1 | |
MYH9 | ENST00000685801.1 | c.3939C>T | p.Ser1313= | synonymous_variant | 30/42 | ||||
MYH9 | ENST00000691109.1 | n.4171C>T | non_coding_transcript_exon_variant | 23/35 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000798 AC: 20AN: 250754Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135646
GnomAD4 exome AF: 0.0000431 AC: 63AN: 1461552Hom.: 0 Cov.: 32 AF XY: 0.0000550 AC XY: 40AN XY: 727060
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74452
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 12, 2021 | See Variant Classification Assertion Criteria. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at