rs1914663
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005411.5(SFTPA1):c.173-115C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0923 in 1,605,492 control chromosomes in the GnomAD database, including 7,613 homozygotes. 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 0.11 ( 1081 hom., cov: 32)
Exomes 𝑓: 0.090 ( 6532 hom. )
Consequence
SFTPA1
NM_005411.5 intron
NM_005411.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.40
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 Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SFTPA1 | NM_005411.5 | c.173-115C>T | intron_variant | ENST00000398636.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SFTPA1 | ENST00000398636.8 | c.173-115C>T | intron_variant | 1 | NM_005411.5 | P1 | |||
SFTPA1 | ENST00000419470.6 | c.218-115C>T | intron_variant | 1 | |||||
SFTPA1 | ENST00000428376.6 | c.173-115C>T | intron_variant | 1 | P1 | ||||
SFTPA1 | ENST00000429958.5 | c.173-115C>T | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.111 AC: 16923AN: 152004Hom.: 1081 Cov.: 32
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GnomAD4 exome AF: 0.0903 AC: 131242AN: 1453370Hom.: 6532 AF XY: 0.0895 AC XY: 64726AN XY: 723188
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GnomAD4 genome ? AF: 0.111 AC: 16951AN: 152122Hom.: 1081 Cov.: 32 AF XY: 0.113 AC XY: 8410AN XY: 74350
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at