rs727504657
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4_ModerateBP6
The NM_004415.4(DSP):āc.2540C>Gā(p.Pro847Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000616 in 1,461,882 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P847L) has been classified as Uncertain significance.
Frequency
Consequence
NM_004415.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DSP | NM_004415.4 | c.2540C>G | p.Pro847Arg | missense_variant | 18/24 | ENST00000379802.8 | |
DSP | NM_001319034.2 | c.2540C>G | p.Pro847Arg | missense_variant | 18/24 | ||
DSP | NM_001008844.3 | c.2540C>G | p.Pro847Arg | missense_variant | 18/24 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DSP | ENST00000379802.8 | c.2540C>G | p.Pro847Arg | missense_variant | 18/24 | 1 | NM_004415.4 | P2 | |
DSP | ENST00000418664.2 | c.2540C>G | p.Pro847Arg | missense_variant | 18/24 | 1 | A2 | ||
DSP | ENST00000710359.1 | c.2540C>G | p.Pro847Arg | missense_variant | 18/24 | A2 | |||
DSP | ENST00000684395.1 | n.1181C>G | non_coding_transcript_exon_variant | 5/5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251430Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135892
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461882Hom.: 0 Cov.: 34 AF XY: 0.00000688 AC XY: 5AN XY: 727244
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jul 03, 2024 | In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Arrhythmogenic right ventricular dysplasia 8;C1854063:Arrhythmogenic cardiomyopathy with wooly hair and keratoderma Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Sep 20, 2022 | - - |
Cardiomyopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Jan 04, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at