rs11564245

Variant names:

• chr12-40429552-G-A
• rs11564245
• ENST00000454784.10:c.2407G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-40429552-G-A
• chr12-40429552-G-C

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_173600.2(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 NM_173600.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.55
• Publications: 0 publications found

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]

ENSG00000258167 (HGNC:):

ACMG classification

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).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173600.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MUC19	NM_173600.2		c.2407G>A	p.Asp803Asn	missense	Exon 21 of 172	NP_775871.2	Q7Z5P9-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MUC19	ENST00000454784.10	TSL:5	c.2407G>A	p.Asp803Asn	missense	Exon 21 of 173	ENSP00000508949.1
	ENSG00000258167	ENST00000552757.2	TSL:5	n.66-9241C>T		intron	N/A
	ENSG00000258167	ENST00000724141.1		n.78-9241C>T		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 8.83e-7 AC: 1 AN: 1131948 Hom.: 0 Cov.: 29 AF XY: 0.00000180 AC XY: 1 AN XY: 554648

African (AFR) AF: 0.00 AC: 0 AN: 23184

American (AMR) AF: 0.00 AC: 0 AN: 24336

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15250

East Asian (EAS) AF: 0.00 AC: 0 AN: 11506

South Asian (SAS) AF: 0.00 AC: 0 AN: 72616

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 27240

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4302

European-Non Finnish (NFE) AF: 0.00000110 AC: 1 AN: 912612

Other (OTH) AF: 0.00 AC: 0 AN: 40902

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Uncertain	-0.040
CADD	Benign	21
DANN	Uncertain	1.0
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs11564245; hg19: chr12-40823354;