chr10-79611798-T-A
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Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP6
The NM_005411.5(SFTPA1):c.-23-5T>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: 𝑓 0.015 ( 0 hom., cov: 33)
Exomes 𝑓: 0.21 ( 5 hom. )
Failed GnomAD Quality Control
Consequence
SFTPA1
NM_005411.5 splice_region, splice_polypyrimidine_tract, intron
NM_005411.5 splice_region, splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.9993
2
Clinical Significance
Conservation
PhyloP100: -1.30
Genes affected
SFTPA1 (HGNC:10798): (surfactant protein A1) This gene encodes a lung surfactant protein that is a member of a subfamily of C-type lectins called collectins. The encoded protein binds specific carbohydrate moieties found on lipids and on the surface of microorganisms. This protein plays an essential role in surfactant homeostasis and in the defense against respiratory pathogens. Mutations in this gene are associated with idiopathic pulmonary fibrosis. Alternate splicing results in multiple transcript variants. [provided by RefSeq, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
BP6
Variant 10-79611798-T-A is Benign according to our data. Variant chr10-79611798-T-A is described in ClinVar as [Benign]. Clinvar id is 3355976.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SFTPA1 | NM_005411.5 | c.-23-5T>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000398636.8 | NP_005402.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SFTPA1 | ENST00000398636.8 | c.-23-5T>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_005411.5 | ENSP00000381633 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 1596AN: 107188Hom.: 0 Cov.: 33 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.206 AC: 181168AN: 877824Hom.: 5 Cov.: 105 AF XY: 0.197 AC XY: 86314AN XY: 439148
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0149 AC: 1594AN: 107304Hom.: 0 Cov.: 33 AF XY: 0.0160 AC XY: 838AN XY: 52510
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Data not reliable, filtered out with message: AS_VQSR
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
SFTPA1-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 25, 2024 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Pathogenic
dbscSNV1_RF
Pathogenic
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: 2
DS_AL_spliceai
Position offset: 5
Find out detailed SpliceAI scores and Pangolin per-transcript scores at