Variant 7-101043210-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001040105.2(MUC17):c.11794G>C(p.Gly3932Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00634 in 1,614,098 control chromosomes in the GnomAD database, including 618 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0078 ( 38 hom., cov: 33)

Exomes 𝑓: 0.0062 ( 580 hom. )

Consequence

MUC17
NM_001040105.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0670

Variant links:

Genes affected

MUC17 (HGNC:16800): (mucin 17, cell surface associated) The protein encoded by this gene is a membrane-bound mucin that provides protection to gut epithelial cells. The encoded protein contains about 60 tandem repeats, with each repeat being around 60 aa. N-glycosylation enables the encoded protein to localize on the cell surface, while the C-terminus interacts with the scaffold protein PDZ domain containing 1 (PDZK1). Two transcript variants, one protein-coding and the other non-protein coding, have been found for this gene. [provided by RefSeq, Nov 2015]

MUC17 links:

MUC17 (HGNC:):

MUC17 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.002008915).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MUC17	NM_001040105.2 linkuse as main transcript	c.11794G>C	p.Gly3932Arg	missense_variant	3/13	ENST00000306151.9	NP_001035194.1	Q685J3-1
MUC17	NR_133665.2 linkuse as main transcript	n.11849G>C		non_coding_transcript_exon_variant	3/12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MUC17	ENST00000306151.9 linkuse as main transcript	c.11794G>C	p.Gly3932Arg	missense_variant	3/13	1	NM_001040105.2	ENSP00000302716.4		Q685J3-1
MUC17	ENST00000379439.3 linkuse as main transcript	n.11794G>C		non_coding_transcript_exon_variant	3/12	1		ENSP00000368751.3		E7EPM4

Frequencies

GnomAD3 genomes

AF:

0.00776

AC:

1181

AN:

152094

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000797

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0177

Gnomad ASJ

AF:

0.000289

Gnomad EAS

AF:

0.114

Gnomad SAS

AF:

0.00641

Gnomad FIN

AF:

0.0184

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000676

Gnomad OTH

AF:

0.00527

GnomAD3 exomes

AF:

0.0142

AC:

3555

AN:

251190

Hom.:

142

AF XY:

0.0129

AC XY:

1748

AN XY:

135718

show subpopulations

Gnomad AFR exome

AF:

0.000677

Gnomad AMR exome

AF:

0.0232

Gnomad ASJ exome

AF:

0.000596

Gnomad EAS exome

AF:

0.117

Gnomad SAS exome

AF:

0.00245

Gnomad FIN exome

AF:

0.0164

Gnomad NFE exome

AF:

0.000784

Gnomad OTH exome

AF:

0.00929

GnomAD4 exome

AF:

0.00619

AC:

9052

AN:

1461886

Hom.:

580

Cov.:

AF XY:

0.00600

AC XY:

4362

AN XY:

727246

show subpopulations

Gnomad4 AFR exome

AF:

0.000299

Gnomad4 AMR exome

AF:

0.0219

Gnomad4 ASJ exome

AF:

0.000612

Gnomad4 EAS exome

AF:

0.158

Gnomad4 SAS exome

AF:

0.00278

Gnomad4 FIN exome

AF:

0.0148

Gnomad4 NFE exome

AF:

0.000360

Gnomad4 OTH exome

AF:

0.00581

GnomAD4 genome

AF:

0.00777

AC:

1182

AN:

152212

Hom.:

Cov.:

AF XY:

0.00962

AC XY:

716

AN XY:

74414

show subpopulations

Gnomad4 AFR

AF:

0.000794

Gnomad4 AMR

AF:

0.0178

Gnomad4 ASJ

AF:

0.000289

Gnomad4 EAS

AF:

0.115

Gnomad4 SAS

AF:

0.00600

Gnomad4 FIN

AF:

0.0184

Gnomad4 NFE

AF:

0.000676

Gnomad4 OTH

AF:

0.00569

Alfa

AF:

0.00483

Hom.:

Bravo

AF:

0.00829

TwinsUK

AF:

0.000539

AC:

ALSPAC

AF:

0.000519

AC:

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000581

AC:

ExAC

AF:

0.0133

AC:

1610

Asia WGS

AF:

0.0430

AC:

149

AN:

3478

EpiCase

AF:

0.000273

EpiControl

AF:

0.000178

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.22

BayesDel_addAF

Benign

-0.79

BayesDel_noAF

Benign

-0.76

CADD

Benign

7.1

DANN

Benign

0.87

DEOGEN2

Benign

0.018

Eigen

Benign

-0.75

Eigen_PC

Benign

-0.98

FATHMM_MKL

Benign

0.012

LIST_S2

Benign

0.40

MetaRNN

Benign

0.0020

MetaSVM

Benign

-0.91

MutationAssessor

Benign

1.3

PrimateAI

Benign

0.17

PROVEAN

Benign

-0.070

REVEL

Benign

0.030

Sift

Benign

0.23

Polyphen

1.0

Vest4

0.026

MutPred

0.28

Loss of loop (P = 0.0203);

ClinPred

0.0094

GERP RS

-0.77

Varity_R

0.040

gMVP

0.021

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