19-9040162-T-C

Variant names:

• chr19-9040162-T-C
• rs6511838
• NM_001414686.1:c.83-4094A>G

Variant summary

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

The NM_001414686.1(MUC16):​c.83-4094A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 151,892 control chromosomes in the GnomAD database, including 40,260 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 0.72 (40260 hom., cov: 31)
• Consequence: MUC16 NM_001414686.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.677
• Publications: 6 publications found

Genes affected

MUC16 (HGNC:15582): (mucin 16, cell surface associated) This gene encodes a protein that is a member of the mucin family. Mucins are high molecular weight, O-glycosylated proteins that play an important role in forming a protective mucous barrier, and are found on the apical surfaces of the epithelia. The encoded protein is a membrane-tethered mucin that contains an extracellular domain at its amino terminus, a large tandem repeat domain, and a transmembrane domain with a short cytoplasmic domain. The amino terminus is highly glycosylated, while the repeat region contains 156 amino acid repeats unit that are rich in serines, threonines, and prolines. Interspersed within the repeats are Sea urchin sperm protein Enterokinase and Agrin (SEA) modules, leucine-rich repeats and ankyrin (ANK) repeats. These regions together form the ectodomain, and there is a potential cleavage site found near an SEA module close to the transmembrane domain. This protein is thought to play a role in forming a barrier, protecting epithelial cells from pathogens. Products of this gene have been used as a marker for different cancers, with higher expression levels associated with poorer outcomes. [provided by RefSeq, May 2017]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001414686.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MUC16	NM_001414686.1		c.83-4094A>G		intron	N/A	NP_001401615.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.718 AC: 108909 AN: 151772 Hom.: 40209 Cov.: 31

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.718 AC: 109016 AN: 151892 Hom.: 40260 Cov.: 31 AF XY: 0.714 AC XY: 52993 AN XY: 74182

African (AFR) AF: 0.914 AC: 37957 AN: 41510

American (AMR) AF: 0.664 AC: 10113 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2109 AN: 3466

East Asian (EAS) AF: 0.562 AC: 2869 AN: 5102

South Asian (SAS) AF: 0.583 AC: 2805 AN: 4814

European-Finnish (FIN) AF: 0.681 AC: 7166 AN: 10524

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.645 AC: 43819 AN: 67952

Other (OTH) AF: 0.682 AC: 1434 AN: 2102

Alfa AF: 0.655 Hom.: 66964

Bravo AF: 0.725

Asia WGS AF: 0.559 AC: 1946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.6
DANN	Benign	0.51
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs6511838; hg19: chr19-9150838;