rs7396030

Variant names:

• chr11-1085368-A-G
• rs7396030
• ENST00000675028.1:c.2219+45A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-1085368-A-G
• chr11-1085368-A-T

Variant summary

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

The NM_002457.5(MUC2):​c.2219+45A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.764 in 1,568,748 control chromosomes in the GnomAD database, including 462,936 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 0.71 (38734 hom., cov: 29)
  • Exomes 𝑓: 0.77 (424202 hom.)
• Consequence: MUC2 NM_002457.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MUC2	NM_002457.5	c.2219+45A>G		intron_variant	Intron 16 of 57		NP_002448.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MUC2	ENST00000675028.1	c.2219+45A>G		intron_variant	Intron 16 of 29			ENSP00000502432.1
MUC2	ENST00000361558.7	n.2246+45A>G		intron_variant	Intron 16 of 48	5

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107045 AN: 151458 Hom.: 38729 Cov.: 29

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.866

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.851

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.799

Gnomad OTH AF: 0.725

GnomAD4 exome AF: 0.770 AC: 1091318 AN: 1417176 Hom.: 424202 Cov.: 27 AF XY: 0.768 AC XY: 540051 AN XY: 703444

Gnomad4 AFR exome AF: 0.560

Gnomad4 AMR exome AF: 0.617

Gnomad4 ASJ exome AF: 0.843

Gnomad4 EAS exome AF: 0.580

Gnomad4 SAS exome AF: 0.635

Gnomad4 FIN exome AF: 0.762

Gnomad4 NFE exome AF: 0.799

Gnomad4 OTH exome AF: 0.760

GnomAD4 genome AF: 0.707 AC: 107094 AN: 151572 Hom.: 38734 Cov.: 29 AF XY: 0.703 AC XY: 52023 AN XY: 74034

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.667

Gnomad4 ASJ AF: 0.851

Gnomad4 EAS AF: 0.578

Gnomad4 SAS AF: 0.635

Gnomad4 FIN AF: 0.768

Gnomad4 NFE AF: 0.799

Gnomad4 OTH AF: 0.725

Alfa AF: 0.790 Hom.: 63685

Bravo AF: 0.693

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7396030; hg19: chr11-1083364;