NM_032578.4:c.2410G>A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_032578.4(MYPN):c.2410G>A(p.Gly804Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0253 in 1,613,978 control chromosomes in the GnomAD database, including 656 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_032578.4 missense
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.2410G>A | p.Gly804Arg | missense_variant | Exon 11 of 20 | ENST00000358913.10 | NP_115967.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0181 AC: 2749AN: 152026Hom.: 33 Cov.: 32
GnomAD3 exomes AF: 0.0183 AC: 4584AN: 251128Hom.: 65 AF XY: 0.0181 AC XY: 2451AN XY: 135714
GnomAD4 exome AF: 0.0260 AC: 38079AN: 1461834Hom.: 623 Cov.: 37 AF XY: 0.0255 AC XY: 18567AN XY: 727216
GnomAD4 genome AF: 0.0181 AC: 2749AN: 152144Hom.: 33 Cov.: 32 AF XY: 0.0165 AC XY: 1224AN XY: 74404
ClinVar
Submissions by phenotype
not specified Benign:7
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p.Gly804Arg in exon 12 of MYPN: This variant is not expected to have clinical si gnificance because it has been identified in 3.5% (301/8600) of European America n chromosomes from a broad population by the NHLBI Exome Sequencing Project (htt p://evs.gs.washington.edu/EVS; dbSNP rs62620248). -
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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. -
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Dilated cardiomyopathy 1KK Benign:3
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not provided Benign:2Other:1
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Cardiovascular phenotype Benign:1
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at