chr6-117539336-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_001366458.2(DCBLD1):c.1058C>A(p.Ser353Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000143 in 1,607,034 control chromosomes in the GnomAD database, including 3 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00012 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00015 ( 3 hom. )
Consequence
DCBLD1
NM_001366458.2 missense
NM_001366458.2 missense
Scores
4
10
4
Clinical Significance
Conservation
PhyloP100: 3.34
Genes affected
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ACMG classification
Classification made for transcript
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.1058C>A | p.Ser353Tyr | missense_variant | 9/15 | ENST00000338728.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCBLD1 | ENST00000338728.10 | c.1058C>A | p.Ser353Tyr | missense_variant | 9/15 | 5 | NM_001366458.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152130Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000110 AC: 27AN: 244632Hom.: 0 AF XY: 0.000113 AC XY: 15AN XY: 132456
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GnomAD4 exome AF: 0.000145 AC: 211AN: 1454786Hom.: 3 Cov.: 30 AF XY: 0.000145 AC XY: 105AN XY: 723712
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GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152248Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74442
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 30, 2023 | The c.1058C>A (p.S353Y) alteration is located in exon 9 (coding exon 9) of the DCBLD1 gene. This alteration results from a C to A substitution at nucleotide position 1058, causing the serine (S) at amino acid position 353 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Pathogenic
Cadd
Uncertain
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
M_CAP
Pathogenic
D
MetaRNN
Uncertain
D;D
MetaSVM
Pathogenic
D
MutationAssessor
Uncertain
M;M
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Pathogenic
Sift
Uncertain
D;D
Sift4G
Benign
T;D
Polyphen
D;D
Vest4
MutPred
Loss of disorder (P = 0.015);Loss of disorder (P = 0.015);
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at