rs754354210
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 1P and 7B. PP2BP4_ModerateBP6BS2
The NM_002473.6(MYH9):āc.2719A>Gā(p.Thr907Ala) variant causes a missense change. The variant allele was found at a frequency of 0.0000304 in 1,611,706 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. T907T) has been classified as Likely benign.
Frequency
Consequence
NM_002473.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYH9 | NM_002473.6 | c.2719A>G | p.Thr907Ala | missense_variant | 22/41 | ENST00000216181.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYH9 | ENST00000216181.11 | c.2719A>G | p.Thr907Ala | missense_variant | 22/41 | 1 | NM_002473.6 | P1 | |
MYH9 | ENST00000685801.1 | c.2782A>G | p.Thr928Ala | missense_variant | 23/42 | ||||
MYH9 | ENST00000495928.1 | n.269A>G | non_coding_transcript_exon_variant | 2/2 | 2 | ||||
MYH9 | ENST00000691109.1 | n.3014A>G | non_coding_transcript_exon_variant | 16/35 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152168Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000280 AC: 7AN: 249764Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135174
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1459538Hom.: 0 Cov.: 32 AF XY: 0.0000289 AC XY: 21AN XY: 726208
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152168Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74334
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 05, 2023 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Feb 01, 2022 | In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jul 01, 2016 | p.Thr907Ala in exon 22 of MYH9: This variant is not expected to have clinical si gnificance because the threonine (Thr) at position 907 is not conserved in evolu tionary distant species, with over 10 species (reptiles, amphibians, fish) havin g an alanine (Ala) at this position. Additional computational prediction tools suggest that this variant may not impact the protein. This variant has been iden tified in 4/66268 European chromosomes by the Exome Aggregation Consortium (ExAC , http://exac.broadinstitute.org; dbSNP rs754354210). In summary, these data ind icate that this variant is likely benign. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at