chr12-40416791-C-T

Variant names:

• chr12-40416791-C-T
• rs1820545
• ENST00000454784.10:c.1321+432C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173600.2(MUC19):​c.1321+432C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.564 in 151,786 control chromosomes in the GnomAD database, including 24,255 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 0.56 (24255 hom., cov: 32)
• Consequence: MUC19 NM_173600.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.354
• Publications: 8 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

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.1321+432C>T		intron	N/A	NP_775871.2	Q7Z5P9-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MUC19	ENST00000454784.10	TSL:5	c.1321+432C>T		intron	N/A	ENSP00000508949.1
	ENSG00000258167	ENST00000552757.2	TSL:5	n.157+3429G>A		intron	N/A
	MUC19	ENST00000676020.2		n.1374+432C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85507 AN: 151668 Hom.: 24244 Cov.: 32

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.555

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.564 AC: 85566 AN: 151786 Hom.: 24255 Cov.: 32 AF XY: 0.564 AC XY: 41790 AN XY: 74150

African (AFR) AF: 0.573 AC: 23705 AN: 41394

American (AMR) AF: 0.534 AC: 8120 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1844 AN: 3468

East Asian (EAS) AF: 0.468 AC: 2415 AN: 5156

South Asian (SAS) AF: 0.618 AC: 2978 AN: 4816

European-Finnish (FIN) AF: 0.528 AC: 5570 AN: 10550

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.578 AC: 39212 AN: 67884

Other (OTH) AF: 0.552 AC: 1165 AN: 2110

Alfa AF: 0.568 Hom.: 48523

Bravo AF: 0.557

Asia WGS AF: 0.511 AC: 1775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.56
DANN	Benign	0.55
PhyloP100		-0.35
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1820545; hg19: chr12-40810593;