Variant chr6-30952347-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_080870.4(MUCL3):c.3883G>A(p.Glu1295Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 1,614,074 control chromosomes in the GnomAD database, including 15,343 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.091 ( 801 hom., cov: 32)

Exomes 𝑓: 0.13 ( 14542 hom. )

Consequence

MUCL3
NM_080870.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.989

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:

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:

HCG21 (HGNC:):

HCG21 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0015239418).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MUCL3	NM_080870.4 linkuse as main transcript	c.3883G>A	p.Glu1295Lys	missense_variant	2/3	ENST00000462446.6	NP_543146.2
HCG21	NR_138040.1 linkuse as main transcript	n.256+15C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
MUCL3	ENST00000462446.6 linkuse as main transcript	c.3883G>A	p.Glu1295Lys	missense_variant	2/3	5	NM_080870.4	ENSP00000417182.1	E9PEI6
MUCL3	ENST00000636043.1 linkuse as main transcript	c.4084G>A	p.Glu1362Lys	missense_variant	5/6	5		ENSP00000490368.1	A0A1B0GV46
SFTA2	ENST00000634371.1 linkuse as main transcript	c.-9+15C>T		intron_variant		5		ENSP00000489572.1	A0A0U1RRK6
HCG21	ENST00000419481.1 linkuse as main transcript	n.224+720C>T		intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.0909

AC:

13819

AN:

152096

Hom.:

801

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0619

Gnomad AMI

AF:

0.144

Gnomad AMR

AF:

0.0368

Gnomad ASJ

AF:

0.0654

Gnomad EAS

AF:

0.0200

Gnomad SAS

AF:

0.0130

Gnomad FIN

AF:

0.0764

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.135

Gnomad OTH

AF:

0.0703

GnomAD3 exomes

AF:

0.0804

AC:

20202

AN:

251246

Hom.:

1183

AF XY:

0.0795

AC XY:

10793

AN XY:

135816

show subpopulations

Gnomad AFR exome

AF:

0.0636

Gnomad AMR exome

AF:

0.0314

Gnomad ASJ exome

AF:

0.0633

Gnomad EAS exome

AF:

0.0203

Gnomad SAS exome

AF:

0.0143

Gnomad FIN exome

AF:

0.0755

Gnomad NFE exome

AF:

0.128

Gnomad OTH exome

AF:

0.0827

GnomAD4 exome

AF:

0.129

AC:

189048

AN:

1461860

Hom.:

14542

Cov.:

AF XY:

0.126

AC XY:

91444

AN XY:

727236

show subpopulations

Gnomad4 AFR exome

AF:

0.0617

Gnomad4 AMR exome

AF:

0.0326

Gnomad4 ASJ exome

AF:

0.0669

Gnomad4 EAS exome

AF:

0.0126

Gnomad4 SAS exome

AF:

0.0157

Gnomad4 FIN exome

AF:

0.0792

Gnomad4 NFE exome

AF:

0.153

Gnomad4 OTH exome

AF:

0.115

GnomAD4 genome

AF:

0.0909

AC:

13829

AN:

152214

Hom.:

801

Cov.:

AF XY:

0.0841

AC XY:

6256

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.0621

Gnomad4 AMR

AF:

0.0366

Gnomad4 ASJ

AF:

0.0654

Gnomad4 EAS

AF:

0.0201

Gnomad4 SAS

AF:

0.0129

Gnomad4 FIN

AF:

0.0764

Gnomad4 NFE

AF:

0.135

Gnomad4 OTH

AF:

0.0691

Alfa

AF:

0.118

Hom.:

1391

Bravo

AF:

0.0889

TwinsUK

AF:

0.169

AC:

625

ALSPAC

AF:

0.162

AC:

623

ESP6500AA

AF:

0.0699

AC:

308

ESP6500EA

AF:

0.132

AC:

1135

ExAC

AF:

0.0801

AC:

9720

Asia WGS

AF:

0.0180

AC:

AN:

3478

EpiCase

AF:

0.130

EpiControl

AF:

0.120

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.067

BayesDel_addAF

Benign

-0.84

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.018

DANN

Benign

0.58

DEOGEN2

Benign

0.0030

T;T;T

Eigen

Benign

-1.8

Eigen_PC

Benign

-1.9

FATHMM_MKL

Benign

0.0042

LIST_S2

Benign

0.40

T;T;T

MetaRNN

Benign

0.0015

T;T;T

MetaSVM

Benign

-0.97

PrimateAI

Benign

0.23

PROVEAN

Benign

-0.23

.;N;.

REVEL

Benign

0.0050

Sift4G

Benign

0.31

.;T;T

Polyphen

0.032

.;B;.

Vest4

0.067, 0.010

MPC

0.61

ClinPred

0.000037

GERP RS

-7.2

Varity_R

0.019

gMVP

0.11

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over