rs200637980
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS1
The NM_002474.3(MYH11):c.2653-6G>C 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 0.0000477 in 1,613,940 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_002474.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYH11 | NM_001040113.2 | c.2674-6G>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000452625.7 | |||
MYH11 | NM_002474.3 | c.2653-6G>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000300036.6 | |||
MYH11 | NM_001040114.2 | c.2674-6G>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
MYH11 | NM_022844.3 | c.2653-6G>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYH11 | ENST00000300036.6 | c.2653-6G>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_002474.3 | P3 | |||
MYH11 | ENST00000452625.7 | c.2674-6G>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001040113.2 | ||||
ENST00000577048.1 | n.514+11C>G | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.000289 AC: 44AN: 152228Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000677 AC: 17AN: 251268Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135804
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1461594Hom.: 0 Cov.: 30 AF XY: 0.0000193 AC XY: 14AN XY: 727090
GnomAD4 genome ? AF: 0.000289 AC: 44AN: 152346Hom.: 0 Cov.: 32 AF XY: 0.000282 AC XY: 21AN XY: 74506
ClinVar
Submissions by phenotype
Familial thoracic aortic aneurysm and aortic dissection Benign:2
Benign, criteria provided, single submitter | clinical testing | All of Us Research Program, National Institutes of Health | Feb 05, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Feb 10, 2019 | - - |
Aortic aneurysm, familial thoracic 4 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 06, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 12, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at