rs10902081

chr11-1081813-T-Cchr11-1081813-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002457.5(MUC2):c.1000+26T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 1,538,258 control chromosomes in the GnomAD database, including 243,008 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 0.61 (29367 hom., cov: 34)
  • Exomes 𝑓: 0.55 (213641 hom.)
• Consequence: MUC2 NM_002457.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MUC2	NM_002457.5	c.1000+26T>C		intron_variant		ENST00000713550.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MUC2	ENST00000675028.1	c.1000+26T>C		intron_variant				P3
MUC2	ENST00000361558.7	n.1027+26T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92948 AN: 152034 Hom.: 29325 Cov.: 34

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.582

GnomAD4 exome AF: 0.550 AC: 761901 AN: 1386106 Hom.: 213641 Cov.: 47 AF XY: 0.552 AC XY: 375547 AN XY: 680214

Gnomad4 AFR exome AF: 0.743

Gnomad4 AMR exome AF: 0.750

Gnomad4 ASJ exome AF: 0.508

Gnomad4 EAS exome AF: 0.800

Gnomad4 SAS exome AF: 0.684

Gnomad4 FIN exome AF: 0.537

Gnomad4 NFE exome AF: 0.520

Gnomad4 OTH exome AF: 0.566

GnomAD4 genome AF: 0.612 AC: 93050 AN: 152152 Hom.: 29367 Cov.: 34 AF XY: 0.615 AC XY: 45771 AN XY: 74374

Gnomad4 AFR AF: 0.738

Gnomad4 AMR AF: 0.687

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.833

Gnomad4 SAS AF: 0.686

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.585

Alfa AF: 0.486 Hom.: 3026

Bravo AF: 0.630

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10902081; hg19: chr11-1079809;