chr7-34955339-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001366673.1(DPY19L1):c.1208T>C(p.Leu403Pro) variant causes a missense change. The variant allele was found at a frequency of 0.00000996 in 1,606,886 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 (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 30)
Exomes 𝑓: 0.000010 ( 0 hom. )
Consequence
DPY19L1
NM_001366673.1 missense
NM_001366673.1 missense
Scores
5
8
Clinical Significance
Conservation
PhyloP100: 5.01
Genes affected
DPY19L1 (HGNC:22205): (dpy-19 like C-mannosyltransferase 1) Predicted to enable mannosyltransferase activity. Predicted to be involved in protein C-linked glycosylation via 2'-alpha-mannosyl-L-tryptophan. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.2509455).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DPY19L1 | NM_001366673.1 | c.1208T>C | p.Leu403Pro | missense_variant | 12/22 | ENST00000638088.2 | |
DPY19L1 | NM_015283.2 | c.989T>C | p.Leu330Pro | missense_variant | 12/22 | ||
DPY19L1 | XM_011515246.4 | c.1121T>C | p.Leu374Pro | missense_variant | 11/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DPY19L1 | ENST00000638088.2 | c.1208T>C | p.Leu403Pro | missense_variant | 12/22 | 5 | NM_001366673.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151954Hom.: 0 Cov.: 30
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GnomAD3 exomes AF: 0.0000500 AC: 12AN: 240100Hom.: 0 AF XY: 0.0000230 AC XY: 3AN XY: 130610
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GnomAD4 exome AF: 0.0000103 AC: 15AN: 1454932Hom.: 0 Cov.: 29 AF XY: 0.00000414 AC XY: 3AN XY: 724154
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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 | Aug 10, 2021 | The c.989T>C (p.L330P) alteration is located in exon 12 (coding exon 12) of the DPY19L1 gene. This alteration results from a T to C substitution at nucleotide position 989, causing the leucine (L) at amino acid position 330 to be replaced by a proline (P). 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
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D
PrimateAI
Uncertain
T
Polyphen
0.90
.;P;.
Vest4
0.50
MutPred
0.62
.;Gain of relative solvent accessibility (P = 0.0082);.;
MVP
0.52
MPC
0.63
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at