Variant 7-100958760-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_005960.2(MUC3A):c.6981G>A(p.Ser2327Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000861 in 800,064 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.18 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00070 ( 0 hom. )

Consequence

MUC3A
NM_005960.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -5.09

Variant links:

Genes affected

MUC3A (HGNC:7513): (mucin 3A, cell surface associated) The mucin genes encode epithelial glycoproteins, some of which are secreted and some membrane bound. Each of the genes contains at least one large domain of tandemly repeated sequence that encodes the peptide sequence rich in serine and/or threonine residues, which carries most of the O-linked glycosylation (Gendler and Spicer, 1995 [PubMed 7778880]).[supplied by OMIM, Aug 2008]

MUC3A links:

LOC105375431 (HGNC:):

LOC105375431 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.03).

BP6

Variant 7-100958760-G-A is Benign according to our data. Variant chr7-100958760-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2657783.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-5.09 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MUC3A	NM_005960.2 linkuse as main transcript	c.6981G>A	p.Ser2327Ser	synonymous_variant	2/12	ENST00000379458.9	NP_005951.1	Q02505-1Q9H3Q6
LOC105375431	XR_007060457.1 linkuse as main transcript	n.43+3513C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
MUC3A	ENST00000379458.9 linkuse as main transcript	c.6981G>A	p.Ser2327Ser	synonymous_variant	2/12	5	NM_005960.2	ENSP00000368771.5	Q02505-1
MUC3A	ENST00000483366.5 linkuse as main transcript	c.6981G>A	p.Ser2327Ser	synonymous_variant	2/11	5		ENSP00000483541.1	Q02505-5
MUC3A	ENST00000414964.5 linkuse as main transcript	n.795G>A		non_coding_transcript_exon_variant	1/10	5		ENSP00000393306.2	A0A182DWF7

Frequencies

GnomAD3 genomes

AF:

0.180

AC:

128

AN:

712

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0538

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0333

Gnomad ASJ

AF:

0.333

Gnomad EAS

AF:

0.118

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.261

Gnomad NFE

AF:

0.224

Gnomad OTH

AF:

0.200

GnomAD3 exomes

AF:

0.0000850

AC:

AN:

164754

Hom.:

AF XY:

0.000117

AC XY:

AN XY:

94286

show subpopulations

Gnomad AFR exome

AF:

0.000121

Gnomad AMR exome

AF:

0.0000888

Gnomad ASJ exome

AF:

0.000259

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000843

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000890

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000702

AC:

561

AN:

799350

Hom.:

Cov.:

102

AF XY:

0.000721

AC XY:

277

AN XY:

384338

show subpopulations

Gnomad4 AFR exome

AF:

0.000187

Gnomad4 AMR exome

AF:

0.000382

Gnomad4 ASJ exome

AF:

0.0107

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000253

Gnomad4 FIN exome

AF:

0.00367

Gnomad4 NFE exome

AF:

0.000525

Gnomad4 OTH exome

AF:

0.000815

GnomAD4 genome

AF:

0.179

AC:

128

AN:

714

Hom.:

Cov.:

AF XY:

0.203

AC XY:

AN XY:

374

show subpopulations

Gnomad4 AFR

AF:

0.0530

Gnomad4 AMR

AF:

0.0333

Gnomad4 ASJ

AF:

0.333

Gnomad4 EAS

AF:

0.118

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.261

Gnomad4 NFE

AF:

0.224

Gnomad4 OTH

AF:

0.200

Alfa

AF:

0.500

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Aug 01, 2023

MUC3A: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

8.9

DANN

Benign

0.64

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over