rs4729656

chr7-101058329-T-Achr7-101058329-T-Cchr7-101058329-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001040105.2(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 NM_001040105.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

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)

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MUC17	NM_001040105.2	c.*285T>A		3_prime_UTR_variant	13/13	ENST00000306151.9
MUC17	NR_133665.2	n.13670T>A		non_coding_transcript_exon_variant	12/12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MUC17	ENST00000306151.9	c.*285T>A		3_prime_UTR_variant	13/13	1	NM_001040105.2	P1
RN7SKP54	ENST00000410704.1	n.31T>A		non_coding_transcript_exon_variant	1/1
MUC17	ENST00000379439.3	c.*826T>A		3_prime_UTR_variant, NMD_transcript_variant	12/12	1

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

Gnomad4 AFR exome AF: 0.671

Gnomad4 AMR exome AF: 0.507

Gnomad4 ASJ exome AF: 0.578

Gnomad4 EAS exome AF: 0.714

Gnomad4 SAS exome AF: 0.683

Gnomad4 FIN exome AF: 0.592

Gnomad4 NFE exome AF: 0.630

Gnomad4 OTH exome AF: 0.621

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

Gnomad4 AFR AF: 0.673

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.567

Gnomad4 EAS AF: 0.699

Gnomad4 SAS AF: 0.646

Gnomad4 FIN AF: 0.579

Gnomad4 NFE AF: 0.617

Gnomad4 OTH AF: 0.589

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.2
Dann	Benign	0.45

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

Other links and lift over

dbSNP: rs4729656; hg19: chr7-100701610;