11-1081883-T-A

Variant names:

• chr11-1081883-T-A
• rs7127117
• ENST00000675028.1:c.1000+96T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000675028.1(MUC2):​c.1000+96T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000046 in 1,304,704 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 35)
  • Exomes 𝑓: 0.0000046 (0 hom.)
• Consequence: MUC2 ENST00000675028.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786
• Publications: 0 publications found

Genes affected

MUC2 (HGNC:7512): (mucin 2, oligomeric mucus/gel-forming) This gene encodes a member of the mucin protein family. Mucins are high molecular weight glycoproteins produced by many epithelial tissues. The protein encoded by this gene is secreted and forms an insoluble mucous barrier that protects the gut lumen. The protein polymerizes into a gel of which 80% is composed of oligosaccharide side chains by weight. The protein features a central domain containing tandem repeats rich in threonine and proline that varies between 50 and 115 copies in different individuals. Downregulation of this gene has been observed in patients with Crohn disease and ulcerative colitis. [provided by RefSeq, Oct 2016]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MUC2	NM_002457.5	c.1000+96T>A		intron_variant	Intron 7 of 57		NP_002448.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MUC2	ENST00000675028.1	c.1000+96T>A		intron_variant	Intron 7 of 29			ENSP00000502432.1
MUC2	ENST00000361558.7	n.1027+96T>A		intron_variant	Intron 7 of 48	5

Frequencies

GnomAD3 genomes Cov.: 35

GnomAD4 exome AF: 0.00000460 AC: 6 AN: 1304704 Hom.: 0 AF XY: 0.00000157 AC XY: 1 AN XY: 635208

African (AFR) AF: 0.00 AC: 0 AN: 30064

American (AMR) AF: 0.00 AC: 0 AN: 31762

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 21872

East Asian (EAS) AF: 0.0000289 AC: 1 AN: 34586

South Asian (SAS) AF: 0.00 AC: 0 AN: 71052

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 35172

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3908

European-Non Finnish (NFE) AF: 0.00000489 AC: 5 AN: 1021936

Other (OTH) AF: 0.00 AC: 0 AN: 54352

GnomAD4 genome Cov.: 35

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.11
DANN	Benign	0.58
PhyloP100		-0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7127117; hg19: chr11-1079879;