Variant 6-30934756-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000636043.1(MUCL3):c.52+82T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.918 in 398,540 control chromosomes in the GnomAD database, including 168,088 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 0.93 ( 65788 hom., cov: 31)

Exomes 𝑓: 0.91 ( 102300 hom. )

Consequence

MUCL3
ENST00000636043.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.724

Variant links:

Genes affected

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:

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:

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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 (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SFTA2	ENST00000634371.1 linkuse as main transcript	c.-8-2961A>G		intron_variant		5
MUCL3	ENST00000636043.1 linkuse as main transcript	c.52+82T>C		intron_variant		5		P4

Frequencies

GnomAD3 genomes

AF:

0.929

AC:

141284

AN:

152140

Hom.:

65727

Cov.:

show subpopulations

Gnomad AFR

AF:

0.976

Gnomad AMI

AF:

0.942

Gnomad AMR

AF:

0.942

Gnomad ASJ

AF:

0.966

Gnomad EAS

AF:

0.984

Gnomad SAS

AF:

0.974

Gnomad FIN

AF:

0.895

Gnomad MID

AF:

0.968

Gnomad NFE

AF:

0.892

Gnomad OTH

AF:

0.942

GnomAD4 exome

AF:

0.911

AC:

224265

AN:

246282

Hom.:

102300

AF XY:

0.910

AC XY:

113517

AN XY:

124802

show subpopulations

Gnomad4 AFR exome

AF:

0.976

Gnomad4 AMR exome

AF:

0.955

Gnomad4 ASJ exome

AF:

0.966

Gnomad4 EAS exome

AF:

0.956

Gnomad4 SAS exome

AF:

0.968

Gnomad4 FIN exome

AF:

0.896

Gnomad4 NFE exome

AF:

0.895

Gnomad4 OTH exome

AF:

0.925

GnomAD4 genome

AF:

0.929

AC:

141404

AN:

152258

Hom.:

65788

Cov.:

AF XY:

0.929

AC XY:

69171

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.976

Gnomad4 AMR

AF:

0.942

Gnomad4 ASJ

AF:

0.966

Gnomad4 EAS

AF:

0.985

Gnomad4 SAS

AF:

0.973

Gnomad4 FIN

AF:

0.895

Gnomad4 NFE

AF:

0.892

Gnomad4 OTH

AF:

0.943

Alfa

AF:

0.903

Hom.:

64493

Bravo

AF:

0.936

Asia WGS

AF:

0.970

AC:

3375

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.99

DANN

Benign

0.59

Splicing

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