NM_001304359.2:c.13596C>T
Variant names:
Variant summary
Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001304359.2(MUC5AC):c.13596C>T(p.Ala4532Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 27)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
MUC5AC
NM_001304359.2 synonymous
NM_001304359.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.34
Publications
0 publications found
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 was made for transcript
Our verdict: Benign. The variant received -7 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 11-1191741-C-T is Benign according to our data. Variant chr11-1191741-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2641166.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-4.34 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001304359.2. You can select a different transcript below to see updated ACMG assignments.
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 128002Hom.: 0 Cov.: 27
GnomAD3 genomes
AF:
AC:
0
AN:
128002
Hom.:
Cov.:
27
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
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Gnomad NFE
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Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 584302Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 318734
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
584302
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
318734
African (AFR)
AF:
AC:
0
AN:
16888
American (AMR)
AF:
AC:
0
AN:
40078
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
20430
East Asian (EAS)
AF:
AC:
0
AN:
35012
South Asian (SAS)
AF:
AC:
0
AN:
66824
European-Finnish (FIN)
AF:
AC:
0
AN:
35614
Middle Eastern (MID)
AF:
AC:
0
AN:
4096
European-Non Finnish (NFE)
AF:
AC:
0
AN:
333578
Other (OTH)
AF:
AC:
0
AN:
31782
GnomAD4 genome 0.00 AC: 0AN: 128002Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0AN XY: 62012
GnomAD4 genome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
128002
Hom.:
Cov.:
27
AF XY:
AC XY:
0
AN XY:
62012
African (AFR)
AF:
AC:
0
AN:
32678
American (AMR)
AF:
AC:
0
AN:
11976
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3248
East Asian (EAS)
AF:
AC:
0
AN:
4224
South Asian (SAS)
AF:
AC:
0
AN:
3920
European-Finnish (FIN)
AF:
AC:
0
AN:
7962
Middle Eastern (MID)
AF:
AC:
0
AN:
182
European-Non Finnish (NFE)
AF:
AC:
0
AN:
61304
Other (OTH)
AF:
AC:
0
AN:
1722
Alfa
AF:
Hom.:
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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