3-195781795-G-GCT

Variant names:

• chr3-195781795-G-GCT
• rs753854746
• NM_018406.7:c.9784_9785insAG

Variant summary

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

The NM_018406.7(MUC4):​c.9784_9785insAG​(p.Thr3262LysfsTer998) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MUC4 NM_018406.7 frameshift
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 0 publications found

Genes affected

MUC4 (HGNC:7514): (mucin 4, cell surface associated) The major constituents of mucus, the viscous secretion that covers epithelial surfaces such as those in the trachea, colon, and cervix, are highly glycosylated proteins called mucins. These glycoproteins play important roles in the protection of the epithelial cells and have been implicated in epithelial renewal and differentiation. This gene encodes an integral membrane glycoprotein found on the cell surface, although secreted isoforms may exist. At least two dozen transcript variants of this gene have been found, although for many of them the full-length transcript has not been determined or they are found only in tumor tissues. This gene contains a region in the coding sequence which has a variable number (>100) of 48 nt tandem repeats. [provided by RefSeq, Jul 2008]

ACMG classification

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MUC4	NM_018406.7	c.9784_9785insAG	p.Thr3262LysfsTer998	frameshift_variant	Exon 2 of 25	ENST00000463781.8	NP_060876.5
MUC4	NM_004532.6	c.83-3341_83-3340insAG		intron_variant	Intron 1 of 23		NP_004523.3
MUC4	NM_138297.5	c.83-7491_83-7490insAG		intron_variant	Intron 1 of 22		NP_612154.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MUC4	ENST00000463781.8	c.9784_9785insAG	p.Thr3262LysfsTer998	frameshift_variant	Exon 2 of 25	5	NM_018406.7	ENSP00000417498.3

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1029472 Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0 AN XY: 499544

African (AFR) AF: 0.00 AC: 0 AN: 24700

American (AMR) AF: 0.00 AC: 0 AN: 25420

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14092

East Asian (EAS) AF: 0.00 AC: 0 AN: 10630

South Asian (SAS) AF: 0.00 AC: 0 AN: 52294

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 19980

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2696

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 841274

Other (OTH) AF: 0.00 AC: 0 AN: 38386

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs753854746; hg19: chr3-195508666;