rs4729655

Variant names:

• chr7-101058170-T-A
• rs4729655
• NM_001040105.2:c.*126T>A

Your query was ambiguous. Multiple possible variants found:

• chr7-101058170-T-A
• chr7-101058170-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001040105.2(MUC17):​c.*126T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MUC17 NM_001040105.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 19 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]

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

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001040105.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MUC17	NM_001040105.2	MANE Select	c.*126T>A		3_prime_UTR	Exon 13 of 13	NP_001035194.1
	MUC17	NR_133665.2		n.13511T>A		non_coding_transcript_exon	Exon 12 of 12

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MUC17	ENST00000306151.9	TSL:1 MANE Select	c.*126T>A		3_prime_UTR	Exon 13 of 13	ENSP00000302716.4
	MUC17	ENST00000379439.3	TSL:1	n.*667T>A		non_coding_transcript_exon	Exon 12 of 12	ENSP00000368751.3
	MUC17	ENST00000379439.3	TSL:1	n.*667T>A		3_prime_UTR	Exon 12 of 12	ENSP00000368751.3

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 664858 Hom.: 0 Cov.: 9 AF XY: 0.00 AC XY: 0 AN XY: 350772

African (AFR) AF: 0.00 AC: 0 AN: 16606

American (AMR) AF: 0.00 AC: 0 AN: 30442

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17806

East Asian (EAS) AF: 0.00 AC: 0 AN: 34004

South Asian (SAS) AF: 0.00 AC: 0 AN: 59470

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 46550

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3110

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 424208

Other (OTH) AF: 0.00 AC: 0 AN: 32662

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.4
DANN	Benign	0.74
PhyloP100		-0.061

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: rs4729655; hg19: chr7-100701451;