17-12715534-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001378306.1(MYOCD):c.-101C>A variant causes a 5 prime UTR premature start codon gain change. The variant allele was found at a frequency of 0.0000322 in 1,613,482 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 Uncertain significance (★).
Frequency
Consequence
NM_001378306.1 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYOCD | ENST00000425538.6 | c.137C>A | p.Ala46Asp | missense_variant | Exon 3 of 14 | 1 | NM_001146312.3 | ENSP00000401678.1 | ||
MYOCD | ENST00000343344.8 | c.137C>A | p.Ala46Asp | missense_variant | Exon 3 of 13 | 1 | ENSP00000341835.4 | |||
MYOCD | ENST00000579237.5 | n.*55C>A | non_coding_transcript_exon_variant | Exon 4 of 5 | 4 | ENSP00000462694.1 | ||||
MYOCD | ENST00000579237.5 | n.*55C>A | 3_prime_UTR_variant | Exon 4 of 5 | 4 | ENSP00000462694.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152214Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 250648Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135488
GnomAD4 exome AF: 0.0000342 AC: 50AN: 1461268Hom.: 0 Cov.: 30 AF XY: 0.0000385 AC XY: 28AN XY: 726914
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152214Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.137C>A (p.A46D) alteration is located in exon 3 (coding exon 3) of the MYOCD gene. This alteration results from a C to A substitution at nucleotide position 137, causing the alanine (A) at amino acid position 46 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at