10-68109732-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_032578.4(MYPN):c.-2+9C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00352 in 452,758 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_032578.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYPN | NM_032578.4 | c.-2+9C>T | intron_variant | Intron 1 of 19 | ENST00000358913.10 | NP_115967.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00834 AC: 1269AN: 152110Hom.: 28 Cov.: 32
GnomAD3 exomes AF: 0.00173 AC: 223AN: 129104Hom.: 3 AF XY: 0.00136 AC XY: 96AN XY: 70476
GnomAD4 exome AF: 0.00108 AC: 326AN: 300530Hom.: 4 Cov.: 0 AF XY: 0.000853 AC XY: 146AN XY: 171226
GnomAD4 genome AF: 0.00834 AC: 1269AN: 152228Hom.: 28 Cov.: 32 AF XY: 0.00770 AC XY: 573AN XY: 74422
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Dilated cardiomyopathy 1KK;C4479186:MYPN-related myopathy Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at