chr3-124905721-A-G

Position:

• chr3-124905721-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
MUC13	NM_033049.4	c.*1022T>C		3_prime_UTR_variant	12/12	ENST00000616727.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MUC13	ENST00000616727.4	c.*1022T>C		3_prime_UTR_variant	12/12	1	NM_033049.4	P1

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

Gnomad4 AFR exome AF: 0.00

Gnomad4 FIN exome AF: 0.155

Gnomad4 NFE exome AF: 0.225

Gnomad4 OTH exome AF: 0.00

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

Gnomad4 AFR AF: 0.0827

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.177

Alfa AF: 0.201 Hom.: 5286

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

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: rs12732; hg19: chr3-124624568;