Variant 7-101032432-C-T 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.1016C>T(p.Thr339Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0164 in 1,609,854 control chromosomes in the GnomAD database, including 1,758 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 0.016 ( 148 hom., cov: 33)

Exomes 𝑓: 0.016 ( 1610 hom. )

Consequence

MUC17
NM_001040105.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.72

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:

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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=0.0010945797).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.168 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.1016C>T	p.Thr339Met	missense_variant	3/13	ENST00000306151.9	NP_001035194.1
MUC17	NR_133665.2 linkuse as main transcript	n.1071C>T		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.1016C>T	p.Thr339Met	missense_variant	3/13	1	NM_001040105.2	ENSP00000302716	P1	Q685J3-1
MUC17	ENST00000379439.3 linkuse as main transcript	c.1016C>T	p.Thr339Met	missense_variant, NMD_transcript_variant	3/12	1		ENSP00000368751

Frequencies

GnomAD3 genomes

AF:

0.0159

AC:

2374

AN:

149008

Hom.:

147

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00224

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0139

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.178

Gnomad SAS

AF:

0.159

Gnomad FIN

AF:

0.0295

Gnomad MID

AF:

0.00360

Gnomad NFE

AF:

0.00136

Gnomad OTH

AF:

0.0181

GnomAD3 exomes

AF:

0.0402

AC:

10064

AN:

250418

Hom.:

640

AF XY:

0.0428

AC XY:

5795

AN XY:

135314

show subpopulations

Gnomad AFR exome

AF:

0.00166

Gnomad AMR exome

AF:

0.0504

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.167

Gnomad SAS exome

AF:

0.140

Gnomad FIN exome

AF:

0.0303

Gnomad NFE exome

AF:

0.00149

Gnomad OTH exome

AF:

0.0239

GnomAD4 exome

AF:

0.0165

AC:

24045

AN:

1460720

Hom.:

1610

Cov.:

AF XY:

0.0198

AC XY:

14352

AN XY:

726612

show subpopulations

Gnomad4 AFR exome

AF:

0.00120

Gnomad4 AMR exome

AF:

0.0449

Gnomad4 ASJ exome

AF:

0.0000384

Gnomad4 EAS exome

AF:

0.164

Gnomad4 SAS exome

AF:

0.135

Gnomad4 FIN exome

AF:

0.0279

Gnomad4 NFE exome

AF:

0.000744

Gnomad4 OTH exome

AF:

0.0247

GnomAD4 genome

AF:

0.0160

AC:

2379

AN:

149134

Hom.:

148

Cov.:

AF XY:

0.0201

AC XY:

1467

AN XY:

72982

show subpopulations

Gnomad4 AFR

AF:

0.00223

Gnomad4 AMR

AF:

0.0140

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.178

Gnomad4 SAS

AF:

0.159

Gnomad4 FIN

AF:

0.0295

Gnomad4 NFE

AF:

0.00136

Gnomad4 OTH

AF:

0.0218

Alfa

AF:

0.00865

Hom.:

TwinsUK

AF:

0.00

AC:

ALSPAC

AF:

0.00234

AC:

ESP6500AA

AF:

0.00295

AC:

ESP6500EA

AF:

0.00116

AC:

ExAC

AF:

0.0393

AC:

4767

Asia WGS

AF:

0.193

AC:

668

AN:

3478

EpiCase

AF:

0.000984

EpiControl

AF:

0.00101

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.091

BayesDel_addAF

Benign

-0.85

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.034

DANN

Benign

0.14

DEOGEN2

Benign

0.017

Eigen

Benign

-1.9

Eigen_PC

Benign

-2.0

FATHMM_MKL

Benign

0.00062

LIST_S2

Benign

0.35

MetaRNN

Benign

0.0011

MetaSVM

Benign

-0.92

MutationAssessor

Benign

-2.1

MutationTaster

Benign

1.0

PrimateAI

Benign

0.22

PROVEAN

Benign

-0.66

REVEL

Benign

0.033

Sift

Benign

0.20

Polyphen

0.014

Vest4

0.040

ClinPred

0.0055

GERP RS

-2.4

Varity_R

0.013

gMVP

0.027

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