rs200509899
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_002471.4(MYH6):c.5566-7C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000959 in 823,808 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_002471.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYH6 | NM_002471.4 | c.5566-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000405093.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYH6 | ENST00000405093.9 | c.5566-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_002471.4 | P1 | |||
MYH6 | ENST00000651452.1 | n.786C>T | non_coding_transcript_exon_variant | 1/3 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 9AN: 150012Hom.: 0 Cov.: 29 FAILED QC
GnomAD3 exomes AF: 0.000293 AC: 60AN: 205012Hom.: 0 AF XY: 0.000287 AC XY: 32AN XY: 111358
GnomAD4 exome AF: 0.0000959 AC: 79AN: 823808Hom.: 0 Cov.: 25 AF XY: 0.0000943 AC XY: 40AN XY: 424184
GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.0000600 AC: 9AN: 150124Hom.: 0 Cov.: 29 AF XY: 0.0000819 AC XY: 6AN XY: 73278
ClinVar
Submissions by phenotype
Hypertrophic cardiomyopathy 14 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 30, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at