17-10628648-C-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6BS2_Supporting
The NM_002470.4(MYH3):c.*5G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000146 in 1,614,068 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 (no stars).
Frequency
Consequence
NM_002470.4 3_prime_UTR
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYH3 | NM_002470.4 | c.*5G>C | 3_prime_UTR_variant | Exon 41 of 41 | ENST00000583535.6 | NP_002461.2 | ||
MYH3 | XM_011523870.4 | c.*5G>C | 3_prime_UTR_variant | Exon 41 of 41 | XP_011522172.1 | |||
MYH3 | XM_011523871.3 | c.*5G>C | 3_prime_UTR_variant | Exon 41 of 41 | XP_011522173.1 | |||
MYH3 | XM_047436127.1 | c.*5G>C | 3_prime_UTR_variant | Exon 43 of 43 | XP_047292083.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYH3 | ENST00000583535 | c.*5G>C | 3_prime_UTR_variant | Exon 41 of 41 | 5 | NM_002470.4 | ENSP00000464317.1 | |||
MYH3 | ENST00000577963.1 | n.370G>C | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 | |||||
MYH3 | ENST00000579928.2 | n.358G>C | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152224Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000112 AC: 28AN: 249480Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135026
GnomAD4 exome AF: 0.000154 AC: 225AN: 1461844Hom.: 0 Cov.: 30 AF XY: 0.000146 AC XY: 106AN XY: 727224
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152224Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74368
ClinVar
Submissions by phenotype
MYH3-related disorder Benign:1
This variant is classified as likely 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