chr12-40490503-G-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_173600.2(MUC19):c.17550G>C(p.Gly5850=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 37)
Consequence
MUC19
NM_173600.2 synonymous
NM_173600.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.48
Genes affected
MUC19 (HGNC:14362): (mucin 19, oligomeric) This gene encodes a member of the gel-forming mucin protein family. Mucin family members are glycoproteins that have tandem repeats which are extensively O-glycosylated. The structural features of mucin proteins are responsible for the gel-like properties of mucus. The encoded protein may be involved in disruption of the ocular surface in Sjogren syndrome. [provided by RefSeq, Apr 2014]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 12-40490503-G-C is Benign according to our data. Variant chr12-40490503-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 2642876.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-3.48 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MUC19 | NM_173600.2 | c.17550G>C | p.Gly5850= | synonymous_variant | 57/172 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUC19 | ENST00000454784.10 | c.17551G>C | p.Asp5851His | missense_variant | 56/173 | 5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 37
GnomAD3 genomes
?
Cov.:
37
GnomAD4 exome Cov.: 62
GnomAD4 exome
Cov.:
62
GnomAD4 genome ? Cov.: 37
GnomAD4 genome
?
Cov.:
37
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2022 | MUC19: PM2:Supporting, BP4, BP7 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.