20-44114814-A-G
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_020433.5(JPH2):āc.2073T>Cā(p.Phe691Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 1,604,238 control chromosomes in the GnomAD database, including 75,081 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_020433.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.324 AC: 49063AN: 151558Hom.: 8541 Cov.: 30
GnomAD3 exomes AF: 0.248 AC: 58346AN: 235182Hom.: 8321 AF XY: 0.242 AC XY: 30531AN XY: 126332
GnomAD4 exome AF: 0.293 AC: 426299AN: 1452562Hom.: 66512 Cov.: 35 AF XY: 0.288 AC XY: 207531AN XY: 721336
GnomAD4 genome AF: 0.324 AC: 49133AN: 151676Hom.: 8569 Cov.: 30 AF XY: 0.316 AC XY: 23400AN XY: 74126
ClinVar
Submissions by phenotype
not specified Benign:3
Phe691Phe in exon 5 of JPH2: This variant is not expected to have clinical signi ficance because it does not alter an amino acid residue and is not located withi n the splice consensus sequence. It has been identified in 44.8% (1973/4404) of African American chromosomes from a broad population by the NHLBI Exome Sequenci ng Project (http://evs.gs.washington.edu/EVS; dbSNP rs6093935). -
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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. -
not provided Benign:1
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Hypertrophic cardiomyopathy 17 Benign:1
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Hypertrophic cardiomyopathy Benign: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