rs370223713
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_017534.6(MYH2):c.2304+7T>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000242 in 1,614,084 control chromosomes in the GnomAD database, including 3 homozygotes. 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_017534.6 splice_region, 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 |
---|---|---|---|---|---|---|---|
MYH2 | NM_017534.6 | c.2304+7T>G | splice_region_variant, intron_variant | ENST00000245503.10 | |||
MYHAS | NR_125367.1 | n.168-34035A>C | intron_variant, non_coding_transcript_variant | ||||
MYH2 | NM_001100112.2 | c.2304+7T>G | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYH2 | ENST00000245503.10 | c.2304+7T>G | splice_region_variant, intron_variant | 1 | NM_017534.6 | P1 | |||
ENST00000399342.6 | n.370+15A>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000322 AC: 49AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00115 AC: 290AN: 251398Hom.: 2 AF XY: 0.000869 AC XY: 118AN XY: 135862
GnomAD4 exome AF: 0.000234 AC: 342AN: 1461880Hom.: 3 Cov.: 31 AF XY: 0.000208 AC XY: 151AN XY: 727248
GnomAD4 genome ? AF: 0.000322 AC: 49AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.000296 AC XY: 22AN XY: 74360
ClinVar
Submissions by phenotype
Myopathy, proximal, and ophthalmoplegia Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jan 13, 2022 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 21, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Feb 13, 2015 | - - |
MYH2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 06, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at