20-44160416-G-C
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_020433.5(JPH2):c.380-9C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00399 in 1,608,122 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_020433.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00412 AC: 627AN: 152252Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00438 AC: 1018AN: 232644Hom.: 5 AF XY: 0.00432 AC XY: 552AN XY: 127698
GnomAD4 exome AF: 0.00398 AC: 5787AN: 1455752Hom.: 22 Cov.: 32 AF XY: 0.00404 AC XY: 2923AN XY: 723876
GnomAD4 genome AF: 0.00411 AC: 627AN: 152370Hom.: 2 Cov.: 32 AF XY: 0.00482 AC XY: 359AN XY: 74510
ClinVar
Submissions by phenotype
not specified Benign:4
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c.380-9C>G in intron 1 of JPH2: This variant is not expected to have clinical si gnificance because it has been identified in 2.9% (78/2666) of Finnish chromosom es by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; db SNP rs111987307). -
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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:2
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Hypertrophic cardiomyopathy 17 Benign:1
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Hypertrophic cardiomyopathy Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at