chr3-98811485-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_080927.4(DCBLD2):c.1433C>T(p.Pro478Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00132 in 1,613,572 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_080927.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DCBLD2 | NM_080927.4 | c.1433C>T | p.Pro478Leu | missense_variant | 11/16 | ENST00000326840.11 | |
DCBLD2 | XM_011512419.3 | c.1205C>T | p.Pro402Leu | missense_variant | 10/15 | ||
DCBLD2 | XM_024453348.2 | c.1115C>T | p.Pro372Leu | missense_variant | 11/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCBLD2 | ENST00000326840.11 | c.1433C>T | p.Pro478Leu | missense_variant | 11/16 | 1 | NM_080927.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00107 AC: 163AN: 152186Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00101 AC: 251AN: 248900Hom.: 0 AF XY: 0.00104 AC XY: 140AN XY: 135046
GnomAD4 exome AF: 0.00134 AC: 1959AN: 1461268Hom.: 2 Cov.: 31 AF XY: 0.00131 AC XY: 953AN XY: 726930
GnomAD4 genome ? AF: 0.00107 AC: 163AN: 152304Hom.: 0 Cov.: 33 AF XY: 0.000832 AC XY: 62AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 20, 2021 | The c.1433C>T (p.P478L) alteration is located in exon 11 (coding exon 11) of the DCBLD2 gene. This alteration results from a C to T substitution at nucleotide position 1433, causing the proline (P) at amino acid position 478 to be replaced by a leucine (L). 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