rs4729656

Variant names:

• chr7-101058329-T-A
• rs4729656
• ENST00000379439.3:n.*826T>A

Your query was ambiguous. Multiple possible variants found:

• chr7-101058329-T-A
• chr7-101058329-T-C
• chr7-101058329-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000306151.9(MUC17):​c.*285T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 283,884 control chromosomes in the GnomAD database, including 56,100 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 0.62 (29676 hom., cov: 32)
  • Exomes 𝑓: 0.63 (26424 hom.)
• Consequence: MUC17 ENST00000306151.9 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 14 publications found

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]

RN7SKP54 (HGNC:45778): (RN7SK pseudogene 54)

MUC12-AS1 (HGNC:40382): (MUC12 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000306151.9. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MUC17	NM_001040105.2	MANE Select	c.*285T>A		3_prime_UTR	Exon 13 of 13	NP_001035194.1
	MUC17	NR_133665.2		n.13670T>A		non_coding_transcript_exon	Exon 12 of 12

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MUC17	ENST00000379439.3	TSL:1	n.*826T>A		non_coding_transcript_exon	Exon 12 of 12	ENSP00000368751.3
	MUC17	ENST00000306151.9	TSL:1 MANE Select	c.*285T>A		3_prime_UTR	Exon 13 of 13	ENSP00000302716.4
	MUC17	ENST00000379439.3	TSL:1	n.*826T>A		3_prime_UTR	Exon 12 of 12	ENSP00000368751.3

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94329 AN: 151978 Hom.: 29653 Cov.: 32

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.591

GnomAD4 exome AF: 0.631 AC: 83124 AN: 131788 Hom.: 26424 Cov.: 2 AF XY: 0.631 AC XY: 42754 AN XY: 67764

African (AFR) AF: 0.671 AC: 3070 AN: 4572

American (AMR) AF: 0.507 AC: 2513 AN: 4956

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2944 AN: 5096

East Asian (EAS) AF: 0.714 AC: 8240 AN: 11544

South Asian (SAS) AF: 0.683 AC: 3551 AN: 5196

European-Finnish (FIN) AF: 0.592 AC: 4739 AN: 8010

Middle Eastern (MID) AF: 0.482 AC: 290 AN: 602

European-Non Finnish (NFE) AF: 0.630 AC: 52384 AN: 83132

Other (OTH) AF: 0.621 AC: 5393 AN: 8680

GnomAD4 genome AF: 0.621 AC: 94394 AN: 152096 Hom.: 29676 Cov.: 32 AF XY: 0.616 AC XY: 45781 AN XY: 74344

African (AFR) AF: 0.673 AC: 27918 AN: 41482

American (AMR) AF: 0.506 AC: 7725 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1966 AN: 3466

East Asian (EAS) AF: 0.699 AC: 3619 AN: 5178

South Asian (SAS) AF: 0.646 AC: 3113 AN: 4820

European-Finnish (FIN) AF: 0.579 AC: 6115 AN: 10570

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.617 AC: 41963 AN: 67990

Other (OTH) AF: 0.589 AC: 1241 AN: 2108

Alfa AF: 0.612 Hom.: 15893

Bravo AF: 0.619

Asia WGS AF: 0.699 AC: 2434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.2
DANN	Benign	0.45
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4729656; hg19: chr7-100701610;