rs1136454
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP7
The NM_005411.5(SFTPA1):c.282G>A(p.Arg94=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000104 in 1,612,532 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00011 ( 0 hom. )
Consequence
SFTPA1
NM_005411.5 synonymous
NM_005411.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.376
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 -5 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP7
Synonymous conserved (PhyloP=-0.376 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SFTPA1 | NM_005411.5 | c.282G>A | p.Arg94= | synonymous_variant | 4/6 | ENST00000398636.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SFTPA1 | ENST00000398636.8 | c.282G>A | p.Arg94= | synonymous_variant | 4/6 | 1 | NM_005411.5 | P1 | |
SFTPA1 | ENST00000419470.6 | c.327G>A | p.Arg109= | synonymous_variant | 4/6 | 1 | |||
SFTPA1 | ENST00000428376.6 | c.282G>A | p.Arg94= | synonymous_variant | 3/5 | 1 | P1 | ||
SFTPA1 | ENST00000429958.5 | c.282G>A | p.Arg94= | synonymous_variant | 3/5 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000659 AC: 10AN: 151780Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00133 AC: 321AN: 241782Hom.: 0 AF XY: 0.00136 AC XY: 178AN XY: 130486
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GnomAD4 exome AF: 0.000107 AC: 157AN: 1460628Hom.: 0 Cov.: 34 AF XY: 0.0000991 AC XY: 72AN XY: 726624
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GnomAD4 genome AF: 0.0000658 AC: 10AN: 151904Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74256
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ClinVar
Not reported inComputational scores
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CADD
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DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at