dbSNP rs11564245: MUC19:p.Asp803Asn (chr12-40429552-G-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The ENST00000454784.10(MUC19):c.2407G>A(p.Asp803Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000883 in 1,131,948 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 32)

Exomes 𝑓: 8.8e-7 ( 0 hom. )

Consequence

MUC19
ENST00000454784.10 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.55

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:

ENSG00000258167 (HGNC:):

ENSG00000258167 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (REVEL=0.108).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	Protein	UniProt
MUC19	NM_173600.2 link	c.2407G>A	p.Asp803Asn	missense_variant	Exon 21 of 172	NP_775871.2	Q7Z5P9-1
LOC105369736	XR_007063562.1 link	n.75-9241C>T		intron_variant	Intron 1 of 4
LOC105369736	XR_944866.1 link	n.75-9241C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MUC19	ENST00000454784.10 link	c.2407G>A	p.Asp803Asn	missense_variant	Exon 21 of 173	5		ENSP00000508949.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

8.83e-7

AC:

AN:

1131948

Hom.:

Cov.:

AF XY:

0.00000180

AC XY:

AN XY:

554648

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

23184

American (AMR)

AF:

0.00

AC:

AN:

24336

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

15250

East Asian (EAS)

AF:

0.00

AC:

AN:

11506

South Asian (SAS)

AF:

0.00

AC:

AN:

72616

European-Finnish (FIN)

AF:

0.00

AC:

AN:

27240

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4302

European-Non Finnish (NFE)

AF:

0.00000110

AC:

AN:

912612

Other (OTH)

AF:

0.00

AC:

AN:

40902

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.675

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Uncertain

-0.040

CADD

Benign

(source)

DANN

Uncertain

1.0

PhyloP100

2.5

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