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GeneBe

11-1161980-C-T

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_001304359.2(MUC5AC):c.285C>T(p.Asp95=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00129 in 1,612,384 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0014 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0013 ( 6 hom. )

Consequence

MUC5AC
NM_001304359.2 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.530
Variant links:
Genes affected
MUC5AC (HGNC:7515): (mucin 5AC, oligomeric mucus/gel-forming) Predicted to be an extracellular matrix structural constituent. Involved in phosphatidylinositol-mediated signaling. Located in cytoplasm; extracellular space; and mucus layer. Implicated in dry eye syndrome. Biomarker of several diseases, including Sjogren's syndrome; biliary tract disease (multiple); cystic fibrosis; eye disease (multiple); and pancreatic cancer (multiple). [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 11-1161980-C-T is Benign according to our data. Variant chr11-1161980-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2641162.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.53 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MUC5ACNM_001304359.2 linkuse as main transcriptc.285C>T p.Asp95= synonymous_variant 4/49 ENST00000621226.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MUC5ACENST00000621226.2 linkuse as main transcriptc.285C>T p.Asp95= synonymous_variant 4/495 NM_001304359.2 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00141
AC:
215
AN:
152208
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000483
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00445
Gnomad ASJ
AF:
0.0144
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00103
Gnomad OTH
AF:
0.00287
GnomAD3 exomes
AF:
0.00152
AC:
375
AN:
246206
Hom.:
0
AF XY:
0.00141
AC XY:
189
AN XY:
134252
show subpopulations
Gnomad AFR exome
AF:
0.000328
Gnomad AMR exome
AF:
0.00280
Gnomad ASJ exome
AF:
0.0152
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000197
Gnomad FIN exome
AF:
0.0000467
Gnomad NFE exome
AF:
0.000928
Gnomad OTH exome
AF:
0.00217
GnomAD4 exome
AF:
0.00128
AC:
1868
AN:
1460058
Hom.:
6
Cov.:
34
AF XY:
0.00125
AC XY:
909
AN XY:
726290
show subpopulations
Gnomad4 AFR exome
AF:
0.000269
Gnomad4 AMR exome
AF:
0.00280
Gnomad4 ASJ exome
AF:
0.0148
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.000232
Gnomad4 FIN exome
AF:
0.0000575
Gnomad4 NFE exome
AF:
0.00106
Gnomad4 OTH exome
AF:
0.00220
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00141
AC:
215
AN:
152326
Hom.:
0
Cov.:
33
AF XY:
0.00148
AC XY:
110
AN XY:
74494
show subpopulations
Gnomad4 AFR
AF:
0.000481
Gnomad4 AMR
AF:
0.00444
Gnomad4 ASJ
AF:
0.0144
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00103
Gnomad4 OTH
AF:
0.00284
Alfa
AF:
0.00213
Hom.:
0
Bravo
AF:
0.00161
Asia WGS
AF:
0.000289
AC:
1
AN:
3478
EpiCase
AF:
0.00136
EpiControl
AF:
0.00101

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 submitterclinical testingCeGaT Center for Human Genetics TuebingenJul 01, 2023MUC5AC: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.69
Cadd
Benign
7.4
Dann
Benign
0.77

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.

Other links and lift over

dbSNP: rs202101385; hg19: chr11-1155597; API