6-83125593-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015018.4(DOP1A):āc.1579T>Cā(p.Ser527Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000372 in 1,613,904 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_015018.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DOP1A | NM_015018.4 | c.1579T>C | p.Ser527Pro | missense_variant | 15/39 | ENST00000349129.7 | NP_055833.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DOP1A | ENST00000349129.7 | c.1579T>C | p.Ser527Pro | missense_variant | 15/39 | 1 | NM_015018.4 | ENSP00000195654.3 | ||
DOP1A | ENST00000369739.7 | c.1552T>C | p.Ser518Pro | missense_variant | 14/39 | 1 | ENSP00000358754.3 | |||
DOP1A | ENST00000237163.9 | c.1552T>C | p.Ser518Pro | missense_variant | 15/40 | 5 | ENSP00000237163.6 | |||
DOP1A | ENST00000604380.1 | c.328T>C | p.Ser110Pro | missense_variant | 3/4 | 5 | ENSP00000474846.1 |
Frequencies
GnomAD3 genomes AF: 0.000177 AC: 27AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251120Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135698
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1461612Hom.: 0 Cov.: 31 AF XY: 0.0000248 AC XY: 18AN XY: 727108
GnomAD4 genome AF: 0.000177 AC: 27AN: 152292Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74470
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 01, 2022 | The c.1552T>C (p.S518P) alteration is located in exon 15 (coding exon 13) of the DOPEY1 gene. This alteration results from a T to C substitution at nucleotide position 1552, causing the serine (S) at amino acid position 518 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at