Variant rs7103978 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_002457.5(MUC2):c.3600A>G(p.Ala1200=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0878 in 1,611,516 control chromosomes in the GnomAD database, including 6,612 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 0.079 ( 512 hom., cov: 34)

Exomes 𝑓: 0.089 ( 6100 hom. )

Consequence

MUC2
NM_002457.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.37

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP7

Synonymous conserved (PhyloP=-1.37 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0933 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.3600A>G	p.Ala1200=	synonymous_variant	26/58	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.3600A>G	p.Ala1200=	synonymous_variant	26/30			ENSP00000502432	P3
MUC2	ENST00000361558.7 linkuse as main transcript	n.3627A>G		non_coding_transcript_exon_variant	26/49	5

Frequencies

GnomAD3 genomes

AF:

0.0786

AC:

11962

AN:

152100

Hom.:

509

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0594

Gnomad AMI

AF:

0.0461

Gnomad AMR

AF:

0.0602

Gnomad ASJ

AF:

0.0357

Gnomad EAS

AF:

0.0609

Gnomad SAS

AF:

0.0542

Gnomad FIN

AF:

0.113

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0953

Gnomad OTH

AF:

0.0738

GnomAD3 exomes

AF:

0.0754

AC:

18488

AN:

245298

Hom.:

784

AF XY:

0.0753

AC XY:

10056

AN XY:

133536

show subpopulations

Gnomad AFR exome

AF:

0.0617

Gnomad AMR exome

AF:

0.0414

Gnomad ASJ exome

AF:

0.0432

Gnomad EAS exome

AF:

0.0660

Gnomad SAS exome

AF:

0.0541

Gnomad FIN exome

AF:

0.114

Gnomad NFE exome

AF:

0.0900

Gnomad OTH exome

AF:

0.0815

GnomAD4 exome

AF:

0.0888

AC:

129548

AN:

1459298

Hom.:

6100

Cov.:

AF XY:

0.0877

AC XY:

63666

AN XY:

725746

show subpopulations

Gnomad4 AFR exome

AF:

0.0630

Gnomad4 AMR exome

AF:

0.0437

Gnomad4 ASJ exome

AF:

0.0425

Gnomad4 EAS exome

AF:

0.0489

Gnomad4 SAS exome

AF:

0.0543

Gnomad4 FIN exome

AF:

0.116

Gnomad4 NFE exome

AF:

0.0958

Gnomad4 OTH exome

AF:

0.0826

GnomAD4 genome

AF:

0.0787

AC:

11981

AN:

152218

Hom.:

512

Cov.:

AF XY:

0.0784

AC XY:

5837

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.0596

Gnomad4 AMR

AF:

0.0601

Gnomad4 ASJ

AF:

0.0357

Gnomad4 EAS

AF:

0.0611

Gnomad4 SAS

AF:

0.0537

Gnomad4 FIN

AF:

0.113

Gnomad4 NFE

AF:

0.0953

Gnomad4 OTH

AF:

0.0754

Alfa

AF:

0.0831

Hom.:

972

Bravo

AF:

0.0739

Asia WGS

AF:

0.0690

AC:

240

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.050

DANN

Benign

0.43

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

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