6-7580705-G-C
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_004415.4(DSP):c.4515G>C(p.Ala1505Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0001 in 1,613,928 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A1505A) has been classified as Likely benign.
Frequency
Consequence
NM_004415.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DSP | NM_004415.4 | c.4515G>C | p.Ala1505Ala | synonymous_variant | Exon 23 of 24 | ENST00000379802.8 | NP_004406.2 | |
DSP | NM_001319034.2 | c.4050+465G>C | intron_variant | Intron 23 of 23 | NP_001305963.1 | |||
DSP | NM_001008844.3 | c.3582+933G>C | intron_variant | Intron 23 of 23 | NP_001008844.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DSP | ENST00000379802.8 | c.4515G>C | p.Ala1505Ala | synonymous_variant | Exon 23 of 24 | 1 | NM_004415.4 | ENSP00000369129.3 | ||
DSP | ENST00000418664.2 | c.3582+933G>C | intron_variant | Intron 23 of 23 | 1 | ENSP00000396591.2 | ||||
DSP | ENST00000710359.1 | c.4050+465G>C | intron_variant | Intron 23 of 23 | ENSP00000518230.1 |
Frequencies
GnomAD3 genomes AF: 0.000171 AC: 26AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000200 AC: 50AN: 249522Hom.: 0 AF XY: 0.000207 AC XY: 28AN XY: 135112
GnomAD4 exome AF: 0.0000930 AC: 136AN: 1461724Hom.: 0 Cov.: 32 AF XY: 0.0000839 AC XY: 61AN XY: 727150
GnomAD4 genome AF: 0.000171 AC: 26AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74348
ClinVar
Submissions by phenotype
Arrhythmogenic cardiomyopathy with wooly hair and keratoderma Benign:1
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Arrhythmogenic right ventricular dysplasia 8;C1854063:Arrhythmogenic cardiomyopathy with wooly hair and keratoderma Benign:1
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Cardiovascular phenotype Benign:1
This alteration is classified as likely 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