rs12732

Variant names:

• chr3-124905721-A-G
• rs12732
• NM_033049.4:c.*1022T>C

Variant summary

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

The NM_033049.4(MUC13):​c.*1022T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,962 control chromosomes in the GnomAD database, including 2,337 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 0.17 (2327 hom., cov: 32)
  • Exomes 𝑓: 0.16 (10 hom.)
• Consequence: MUC13 NM_033049.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.552
• Publications: 7 publications found

Genes affected

MUC13 (HGNC:7511): (mucin 13, cell surface associated) Epithelial mucins, such as MUC13, are a family of secreted and cell surface glycoproteins expressed by ductal and glandular epithelial tissues (Williams et al., 2001 [PubMed 11278439]).[supplied by OMIM, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MUC13	NM_033049.4	c.*1022T>C		3_prime_UTR_variant	Exon 12 of 12	ENST00000616727.4	NP_149038.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MUC13	ENST00000616727.4	c.*1022T>C		3_prime_UTR_variant	Exon 12 of 12	1	NM_033049.4	ENSP00000485028.1

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25265 AN: 152014 Hom.: 2324 Cov.: 32

Gnomad AFR AF: 0.0826

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.179

GnomAD4 exome AF: 0.157 AC: 130 AN: 830 Hom.: 10 Cov.: 0 AF XY: 0.158 AC XY: 66 AN XY: 418

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.155 AC: 121 AN: 782

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.225 AC: 9 AN: 40

Other (OTH) AF: 0.00 AC: 0 AN: 6

GnomAD4 genome AF: 0.166 AC: 25275 AN: 152132 Hom.: 2327 Cov.: 32 AF XY: 0.164 AC XY: 12211 AN XY: 74374

African (AFR) AF: 0.0827 AC: 3432 AN: 41522

American (AMR) AF: 0.186 AC: 2844 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 619 AN: 3466

East Asian (EAS) AF: 0.116 AC: 601 AN: 5176

South Asian (SAS) AF: 0.221 AC: 1066 AN: 4824

European-Finnish (FIN) AF: 0.158 AC: 1671 AN: 10590

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14456 AN: 67988

Other (OTH) AF: 0.177 AC: 374 AN: 2110

Alfa AF: 0.196 Hom.: 11680

Bravo AF: 0.163

Asia WGS AF: 0.182 AC: 635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.4
DANN	Benign	0.27
PhyloP100		0.55
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: rs12732; hg19: chr3-124624568;