7-100952683-G-GAAGTAGTCACCAGTGGCACCAT

Variant names:

• chr7-100952683-G-GAAGTAGTCACCAGTGGCACCAT
• rs1728669681
• NM_005960.2:c.906_907insGTAGTCACCAGTGGCACCATAA

Variant summary

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

The NM_005960.2(MUC3A):​c.906_907insGTAGTCACCAGTGGCACCATAA​(p.Thr303ValfsTer38) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. 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: 48)
• Consequence: MUC3A NM_005960.2 frameshift
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286
• Publications: 0 publications found

Genes affected

MUC3A (HGNC:7513): (mucin 3A, cell surface associated) The mucin genes encode epithelial glycoproteins, some of which are secreted and some membrane bound. Each of the genes contains at least one large domain of tandemly repeated sequence that encodes the peptide sequence rich in serine and/or threonine residues, which carries most of the O-linked glycosylation (Gendler and Spicer, 1995 [PubMed 7778880]).[supplied by OMIM, Aug 2008]

LOC105375431 (HGNC:):

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005960.2. 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
	MUC3A	NM_005960.2	MANE Select	c.906_907insGTAGTCACCAGTGGCACCATAA	p.Thr303ValfsTer38	frameshift	Exon 2 of 12	NP_005951.1	Q02505-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MUC3A	ENST00000379458.9	TSL:5 MANE Select	c.906_907insGTAGTCACCAGTGGCACCATAA	p.Thr303ValfsTer38	frameshift	Exon 2 of 12	ENSP00000368771.5	Q02505-1
	MUC3A	ENST00000483366.5	TSL:5	c.906_907insGTAGTCACCAGTGGCACCATAA	p.Thr303ValfsTer38	frameshift	Exon 2 of 11	ENSP00000483541.1	Q02505-5
	MUC3A	ENST00000868577.1		c.61+3000_61+3001insGTAGTCACCAGTGGCACCATAA		intron	N/A	ENSP00000538636.1

Frequencies

GnomAD3 genomes Cov.: 48

GnomAD4 exome Cov.: 80

GnomAD4 genome Cov.: 48

Alfa AF: 0.000676 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.29

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1728669681; hg19: chr7-100550323;