chr6-117532338-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001366458.2(DCBLD1):c.664C>T(p.Arg222Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,613,602 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 Uncertain significance (★).
Frequency
Consequence
NM_001366458.2 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 |
---|---|---|---|---|---|---|---|
DCBLD1 | NM_001366458.2 | c.664C>T | p.Arg222Cys | missense_variant | 6/15 | ENST00000338728.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCBLD1 | ENST00000338728.10 | c.664C>T | p.Arg222Cys | missense_variant | 6/15 | 5 | NM_001366458.2 | A2 | |
DCBLD1 | ENST00000296955.12 | c.664C>T | p.Arg222Cys | missense_variant | 6/15 | 1 | P2 | ||
DCBLD1 | ENST00000533453.5 | n.687C>T | non_coding_transcript_exon_variant | 4/11 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152202Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250636Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135452
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1461282Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 726924
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152320Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 05, 2021 | The c.664C>T (p.R222C) alteration is located in exon 6 (coding exon 6) of the DCBLD1 gene. This alteration results from a C to T substitution at nucleotide position 664, causing the arginine (R) at amino acid position 222 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