11-1185387-A-T

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_Strong BP6_Moderate BP7

The NM_001304359.2(MUC5AC):c.7242A>T(p.Ser2414=) 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 0.0093 (0 hom., cov: 23)
  • Exomes 𝑓: 0.00066 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MUC5AC NM_001304359.2 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -4.89

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]

ACMG classification

Verdict is Benign. Variant got -7 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=0.69).
• BP6: Variant 11-1185387-A-T is Benign according to our data. Variant chr11-1185387-A-T is described in ClinVar as [Likely_benign]. Clinvar id is 2431070.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-4.89 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MUC5AC	NM_001304359.2	c.7242A>T	p.Ser2414=	synonymous_variant	31/49	ENST00000621226.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MUC5AC	ENST00000621226.2	c.7242A>T	p.Ser2414=	synonymous_variant	31/49	5	NM_001304359.2	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 606 AN: 65368 Hom.: 0 Cov.: 23 FAILED QC

Gnomad AFR AF: 0.0142

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.00802

Gnomad ASJ AF: 0.00398

Gnomad EAS AF: 0.0161

Gnomad SAS AF: 0.00733

Gnomad FIN AF: 0.0119

Gnomad MID AF: 0.0366

Gnomad NFE AF: 0.00676

Gnomad OTH AF: 0.00826

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000664 AC: 317 AN: 477640 Hom.: 0 Cov.: 0 AF XY: 0.000635 AC XY: 168 AN XY: 264420

Gnomad4 AFR exome AF: 0.00154

Gnomad4 AMR exome AF: 0.00234

Gnomad4 ASJ exome AF: 0.000236

Gnomad4 EAS exome AF: 0.000685

Gnomad4 SAS exome AF: 0.000787

Gnomad4 FIN exome AF: 0.0000929

Gnomad4 NFE exome AF: 0.000515

Gnomad4 OTH exome AF: 0.000630

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00928 AC: 607 AN: 65430 Hom.: 0 Cov.: 23 AF XY: 0.00918 AC XY: 299 AN XY: 32554

Gnomad4 AFR AF: 0.0142

Gnomad4 AMR AF: 0.00816

Gnomad4 ASJ AF: 0.00398

Gnomad4 EAS AF: 0.0161

Gnomad4 SAS AF: 0.00735

Gnomad4 FIN AF: 0.0119

Gnomad4 NFE AF: 0.00676

Gnomad4 OTH AF: 0.00815

Alfa AF: 0.193 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Lung adenocarcinoma Benign:1

Likely benign, criteria provided, single submitter

research

Liquid Biopsy and Cancer Interception Group, Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research

Jun 06, 2022

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
Cadd	Benign	0.69

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1479472284; hg19: -;