rs1048371

Positions:

• chr12-54854573-G-T

Variant summary

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

The NM_058173.3(MUCL1):​c.-10G>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 1,609,142 control chromosomes in the GnomAD database, including 194,692 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 0.45 (16353 hom., cov: 31)
  • Exomes 𝑓: 0.49 (178339 hom.)
• Consequence: MUCL1 NM_058173.3 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.504

Genes affected

MUCL1 (HGNC:30588): (mucin like 1) Predicted to be located in Golgi lumen and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

MUCL1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MUCL1	NM_058173.3	c.-10G>T		5_prime_UTR_premature_start_codon_gain_variant	1/4	ENST00000308796.11	NP_477521.1
MUCL1	NM_058173.3	c.-10G>T		5_prime_UTR_variant	1/4	ENST00000308796.11	NP_477521.1
MUCL1	XM_047428272.1	c.-10G>T		5_prime_UTR_premature_start_codon_gain_variant	2/5		XP_047284228.1
MUCL1	XM_047428272.1	c.-10G>T		5_prime_UTR_variant	2/5		XP_047284228.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MUCL1	ENST00000308796.11	c.-10G>T		5_prime_UTR_premature_start_codon_gain_variant	1/4	1	NM_058173.3	ENSP00000311364.5
MUCL1	ENST00000308796.11	c.-10G>T		5_prime_UTR_variant	1/4	1	NM_058173.3	ENSP00000311364.5

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68175 AN: 151726 Hom.: 16332 Cov.: 31

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.838

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.472

GnomAD3 exomes AF: 0.528 AC: 131927 AN: 249818 Hom.: 36908 AF XY: 0.529 AC XY: 71359 AN XY: 134978

Gnomad AFR exome AF: 0.290

Gnomad AMR exome AF: 0.632

Gnomad ASJ exome AF: 0.496

Gnomad EAS exome AF: 0.841

Gnomad SAS exome AF: 0.608

Gnomad FIN exome AF: 0.514

Gnomad NFE exome AF: 0.465

Gnomad OTH exome AF: 0.510

GnomAD4 exome AF: 0.486 AC: 708589 AN: 1457298 Hom.: 178339 Cov.: 32 AF XY: 0.490 AC XY: 355574 AN XY: 725074

Gnomad4 AFR exome AF: 0.294

Gnomad4 AMR exome AF: 0.623

Gnomad4 ASJ exome AF: 0.489

Gnomad4 EAS exome AF: 0.835

Gnomad4 SAS exome AF: 0.607

Gnomad4 FIN exome AF: 0.512

Gnomad4 NFE exome AF: 0.463

Gnomad4 OTH exome AF: 0.494

GnomAD4 genome AF: 0.449 AC: 68232 AN: 151844 Hom.: 16353 Cov.: 31 AF XY: 0.456 AC XY: 33845 AN XY: 74218

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.492

Gnomad4 EAS AF: 0.838

Gnomad4 SAS AF: 0.619

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.477

Alfa AF: 0.461 Hom.: 31189

Bravo AF: 0.446

Asia WGS AF: 0.708 AC: 2457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.8
DANN	Benign	0.77

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: rs1048371; hg19: chr12-55248357;