Genetic Variant ENST00000454784.10:c.20617+56G>A (chr12-40521024-G-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000454784.10(MUC19):c.20617+56G>A variant causes a intron 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

MUC19
ENST00000454784.10 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.737

Publications

0 publications found

Variant links:

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]

MUC19 links:

ENSG00000296211 (HGNC:):

ENSG00000296211 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MUC19	NM_173600.2 link	c.20563+56G>A		intron_variant	Intron 99 of 171		NP_775871.2	Q7Z5P9-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein
MUC19	ENST00000454784.10 link	c.20617+56G>A	intron_variant	Intron 99 of 172	5	ENSP00000508949.1
MUC19	ENST00000398702.7 link	n.253+56G>A	intron_variant	Intron 2 of 6	4
ENSG00000296211	ENST00000737355.1 link	n.441-2007C>T	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

827220

Hom.:

AF XY:

0.00

AC XY:

AN XY:

383330

African (AFR)

AF:

0.00

AC:

AN:

15478

American (AMR)

AF:

0.00

AC:

AN:

1118

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

5202

East Asian (EAS)

AF:

0.00

AC:

AN:

3756

South Asian (SAS)

AF:

0.00

AC:

AN:

16838

European-Finnish (FIN)

AF:

0.00

AC:

AN:

9248

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3242

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

745062

Other (OTH)

AF:

0.00

AC:

AN:

27276

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

1.2

(source)

DANN

Benign

0.37

PhyloP100

-0.74

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over