dbSNP rs3757340: MUCL3:c.*988T>C (chr6-30954105-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_080870.4(MUCL3):c.*988T>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 0.364 in 152,122 control chromosomes in the GnomAD database, including 10,700 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 0.36 ( 10697 hom., cov: 31)

Exomes 𝑓: 0.29 ( 3 hom. )

Consequence

MUCL3
NM_080870.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.497

Publications

30 publications found

Variant links:

Genes affected

MUCL3 (HGNC:21666): (mucin like 3) Predicted to be located in cytoplasm and plasma membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

MUCL3 links:

HCG21 (HGNC:31335): (HLA complex group 21)

HCG21 links:

SFTA2 (HGNC:18386): (surfactant associated 2) Predicted to be located in Golgi apparatus; extracellular region; and transport vesicle. [provided by Alliance of Genome Resources, Apr 2022]

SFTA2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_080870.4. 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
	MUCL3	NM_080870.4	MANE Select	c.*988T>C		3_prime_UTR	Exon 3 of 3	NP_543146.2
	HCG21	NR_138040.1		n.86+672A>G		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MUCL3	ENST00000462446.6	TSL:5 MANE Select	c.*988T>C	3_prime_UTR	Exon 3 of 3	ENSP00000417182.1
HCG21	ENST00000419481.1	TSL:3	n.86+672A>G	intron	N/A
SFTA2	ENST00000634371.2	TSL:5	n.196+672A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.364

AC:

55291

AN:

151946

Hom.:

10673

Cov.:

show subpopulations

Gnomad AFR

AF:

0.446

Gnomad AMI

AF:

0.396

Gnomad AMR

AF:

0.465

Gnomad ASJ

AF:

0.282

Gnomad EAS

AF:

0.430

Gnomad SAS

AF:

0.526

Gnomad FIN

AF:

0.332

Gnomad MID

AF:

0.377

Gnomad NFE

AF:

0.282

Gnomad OTH

AF:

0.396

GnomAD4 exome

AF:

0.293

AC:

AN:

Hom.:

Cov.:

AF XY:

0.321

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.265

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.318

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.364

AC:

55354

AN:

152064

Hom.:

10697

Cov.:

AF XY:

0.372

AC XY:

27650

AN XY:

74318

show subpopulations

African (AFR)

AF:

0.446

AC:

18473

AN:

41446

American (AMR)

AF:

0.466

AC:

7122

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.282

AC:

978

AN:

3470

East Asian (EAS)

AF:

0.430

AC:

2228

AN:

5182

South Asian (SAS)

AF:

0.526

AC:

2530

AN:

4810

European-Finnish (FIN)

AF:

0.332

AC:

3502

AN:

10558

Middle Eastern (MID)

AF:

0.378

AC:

111

AN:

294

European-Non Finnish (NFE)

AF:

0.282

AC:

19198

AN:

67986

Other (OTH)

AF:

0.402

AC:

851

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1738

3476

5214

6952

8690

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

540

1080

1620

2160

2700

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.307

Hom.:

32882

Bravo

AF:

0.374

Asia WGS

AF:

0.545

AC:

1894

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.98

(source)

DANN

Benign

0.68

PhyloP100

-0.50

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over