Variant 11-1075747-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_002457.5(MUC2):c.173C>T(p.Pro58Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.846 in 1,609,964 control chromosomes in the GnomAD database, including 581,143 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.79 ( 48650 hom., cov: 35)

Exomes 𝑓: 0.85 ( 532493 hom. )

Consequence

MUC2
NM_002457.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.903

Variant links:

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]

MUC2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MUC2	NM_002457.5 linkuse as main transcript	c.173C>T	p.Pro58Leu	missense_variant	2/58	ENST00000713550.1	NP_002448.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MUC2	ENST00000675028.1 linkuse as main transcript	c.173C>T	p.Pro58Leu	missense_variant	2/30			ENSP00000502432	P3
MUC2	ENST00000361558.7 linkuse as main transcript	n.200C>T		non_coding_transcript_exon_variant	2/49	5

Frequencies

GnomAD3 genomes

AF:

0.791

AC:

120367

AN:

152094

Hom.:

48625

Cov.:

show subpopulations

Gnomad AFR

AF:

0.637

Gnomad AMI

AF:

0.872

Gnomad AMR

AF:

0.863

Gnomad ASJ

AF:

0.880

Gnomad EAS

AF:

0.532

Gnomad SAS

AF:

0.838

Gnomad FIN

AF:

0.825

Gnomad MID

AF:

0.889

Gnomad NFE

AF:

0.873

Gnomad OTH

AF:

0.828

GnomAD4 exome

AF:

0.852

AC:

1242079

AN:

1457750

Hom.:

532493

Cov.:

AF XY:

0.852

AC XY:

617823

AN XY:

724918

show subpopulations

Gnomad4 AFR exome

AF:

0.625

Gnomad4 AMR exome

AF:

0.891

Gnomad4 ASJ exome

AF:

0.872

Gnomad4 EAS exome

AF:

0.530

Gnomad4 SAS exome

AF:

0.832

Gnomad4 FIN exome

AF:

0.826

Gnomad4 NFE exome

AF:

0.872

Gnomad4 OTH exome

AF:

0.839

GnomAD4 genome

AF:

0.791

AC:

120452

AN:

152214

Hom.:

48650

Cov.:

AF XY:

0.790

AC XY:

58807

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.637

Gnomad4 AMR

AF:

0.864

Gnomad4 ASJ

AF:

0.880

Gnomad4 EAS

AF:

0.533

Gnomad4 SAS

AF:

0.839

Gnomad4 FIN

AF:

0.825

Gnomad4 NFE

AF:

0.873

Gnomad4 OTH

AF:

0.828

Alfa

AF:

0.854

Hom.:

81159

Bravo

AF:

0.786

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Uncertain

-0.060

CADD

Benign

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over