rs1048371

Variant names:

• chr12-54854573-G-T
• rs1048371
• NM_058173.3:c.-10G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_058173.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MUCL1	NM_058173.3	MANE Select	c.-10G>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 4	NP_477521.1
	MUCL1	NM_058173.3	MANE Select	c.-10G>T		5_prime_UTR	Exon 1 of 4	NP_477521.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MUCL1	ENST00000308796.11	TSL:1 MANE Select	c.-10G>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 4	ENSP00000311364.5
	MUCL1	ENST00000308796.11	TSL:1 MANE Select	c.-10G>T		5_prime_UTR	Exon 1 of 4	ENSP00000311364.5
	MUCL1	ENST00000547958.1	TSL:2	n.58G>T		non_coding_transcript_exon	Exon 1 of 2

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

GnomAD2 exomes AF: 0.528 AC: 131927 AN: 249818 AF XY: 0.529

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 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

African (AFR) AF: 0.294 AC: 9780 AN: 33290

American (AMR) AF: 0.623 AC: 27684 AN: 44464

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 12729 AN: 26048

East Asian (EAS) AF: 0.835 AC: 33107 AN: 39652

South Asian (SAS) AF: 0.607 AC: 52265 AN: 86040

European-Finnish (FIN) AF: 0.512 AC: 27336 AN: 53350

Middle Eastern (MID) AF: 0.504 AC: 2894 AN: 5744

European-Non Finnish (NFE) AF: 0.463 AC: 513089 AN: 1108524

Other (OTH) AF: 0.494 AC: 29705 AN: 60186

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

African (AFR) AF: 0.299 AC: 12381 AN: 41416

American (AMR) AF: 0.547 AC: 8345 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1706 AN: 3464

East Asian (EAS) AF: 0.838 AC: 4300 AN: 5132

South Asian (SAS) AF: 0.619 AC: 2977 AN: 4812

European-Finnish (FIN) AF: 0.511 AC: 5380 AN: 10538

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31495 AN: 67914

Other (OTH) AF: 0.477 AC: 1004 AN: 2104

Alfa AF: 0.460 Hom.: 66422

Bravo AF: 0.446

Asia WGS AF: 0.708 AC: 2457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.8
DANN	Benign	0.77
PhyloP100		-0.50
PromoterAI		-0.0098	Neutral
Mutation Taster		=300/0	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: rs1048371; hg19: chr12-55248357;