3-98800651-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_080927.4(DCBLD2):c.1786C>T(p.Arg596Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000384 in 1,613,820 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R596H) has been classified as Uncertain significance.
Frequency
Consequence
NM_080927.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DCBLD2 | NM_080927.4 | c.1786C>T | p.Arg596Cys | missense_variant | 15/16 | ENST00000326840.11 | |
DCBLD2 | XM_011512419.3 | c.1558C>T | p.Arg520Cys | missense_variant | 14/15 | ||
DCBLD2 | XM_024453348.2 | c.1468C>T | p.Arg490Cys | missense_variant | 15/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCBLD2 | ENST00000326840.11 | c.1786C>T | p.Arg596Cys | missense_variant | 15/16 | 1 | NM_080927.4 | P1 | |
DCBLD2 | ENST00000326857.9 | c.1828C>T | p.Arg610Cys | missense_variant | 15/16 | 1 | |||
DCBLD2 | ENST00000496736.1 | n.438C>T | non_coding_transcript_exon_variant | 2/3 | 3 | ||||
ST3GAL6 | ENST00000491912.1 | n.254-771G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000361 AC: 9AN: 249126Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135160
GnomAD4 exome AF: 0.0000383 AC: 56AN: 1461668Hom.: 0 Cov.: 32 AF XY: 0.0000344 AC XY: 25AN XY: 727122
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | The c.1786C>T (p.R596C) alteration is located in exon 15 (coding exon 15) of the DCBLD2 gene. This alteration results from a C to T substitution at nucleotide position 1786, causing the arginine (R) at amino acid position 596 to be replaced by a cysteine (C). 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