chr7-100952833-GCC-G

Variant names:

• chr7-100952833-GCC-G
• rs1584799673
• NM_005960.2:c.1055_1056delCC

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_005960.2(MUC3A):​c.1055_1056delCC​(p.Ala352ValfsTer41) 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: 𝑓 0.25 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00011 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MUC3A NM_005960.2 frameshift
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 2.20

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

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MUC3A	NM_005960.2	c.1055_1056delCC	p.Ala352ValfsTer41	frameshift_variant	Exon 2 of 12	ENST00000379458.9	NP_005951.1
LOC105375431	XR_007060457.1	n.44-6084_44-6083delGG		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MUC3A	ENST00000379458.9	c.1055_1056delCC	p.Ala352ValfsTer41	frameshift_variant	Exon 2 of 12	5	NM_005960.2	ENSP00000368771.5
MUC3A	ENST00000483366.5	c.1055_1056delCC	p.Ala352ValfsTer41	frameshift_variant	Exon 2 of 11	5		ENSP00000483541.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 31833 AN: 128078 Hom.: 0 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.273

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000111 AC: 138 AN: 1243290 Hom.: 0 AF XY: 0.000150 AC XY: 91 AN XY: 605880

Gnomad4 AFR exome AF: 0.0000729

Gnomad4 AMR exome AF: 0.0000738

Gnomad4 ASJ exome AF: 0.0000511

Gnomad4 EAS exome AF: 0.0000345

Gnomad4 SAS exome AF: 0.000704

Gnomad4 FIN exome AF: 0.0000786

Gnomad4 NFE exome AF: 0.0000742

Gnomad4 OTH exome AF: 0.000220

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.248 AC: 31840 AN: 128172 Hom.: 0 Cov.: 0 AF XY: 0.253 AC XY: 15873 AN XY: 62722

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.271

Alfa AF: 0.0187 Hom.: 0

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Lung cancer Pathogenic:1

Jun 15, 2021

Arun Kumar Laboratory, Indian Institute of Science

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: research

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1584799673; hg19: chr7-100550473;