rs2012353
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001172774.2(DPY19L3):c.103+31G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 1,543,030 control chromosomes in the GnomAD database, including 22,499 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.17 ( 2242 hom., cov: 32)
Exomes 𝑓: 0.17 ( 20257 hom. )
Consequence
DPY19L3
NM_001172774.2 intron
NM_001172774.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.29
Genes affected
DPY19L3 (HGNC:27120): (dpy-19 like C-mannosyltransferase 3) Predicted to enable mannosyltransferase activity. Predicted to be involved in protein C-linked glycosylation via 2'-alpha-mannosyl-L-tryptophan. Predicted to be integral component of membrane. Predicted to be active in nuclear inner membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DPY19L3 | NM_001172774.2 | c.103+31G>A | intron_variant | ENST00000392250.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DPY19L3 | ENST00000392250.7 | c.103+31G>A | intron_variant | 5 | NM_001172774.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.171 AC: 25928AN: 151978Hom.: 2237 Cov.: 32
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GnomAD3 exomes AF: 0.173 AC: 41245AN: 238424Hom.: 3568 AF XY: 0.172 AC XY: 22168AN XY: 128964
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GnomAD4 exome AF: 0.169 AC: 235094AN: 1390934Hom.: 20257 Cov.: 22 AF XY: 0.168 AC XY: 116998AN XY: 695688
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GnomAD4 genome ? AF: 0.171 AC: 25950AN: 152096Hom.: 2242 Cov.: 32 AF XY: 0.171 AC XY: 12742AN XY: 74376
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at