chr10-79612475-CG-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_005411.5(SFTPA1):c.292+45del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 1,608,504 control chromosomes in the GnomAD database, including 37,694 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.21 ( 3539 hom., cov: 26)
Exomes 𝑓: 0.21 ( 34155 hom. )
Consequence
SFTPA1
NM_005411.5 intron
NM_005411.5 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.188
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 -10 ACMG points.
BP6
?
Variant 10-79612475-CG-C is Benign according to our data. Variant chr10-79612475-CG-C is described in ClinVar as [Benign]. Clinvar id is 1270909.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SFTPA1 | NM_005411.5 | c.292+45del | intron_variant | ENST00000398636.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SFTPA1 | ENST00000398636.8 | c.292+45del | intron_variant | 1 | NM_005411.5 | P1 | |||
SFTPA1 | ENST00000419470.6 | c.337+45del | intron_variant | 1 | |||||
SFTPA1 | ENST00000428376.6 | c.292+45del | intron_variant | 1 | P1 | ||||
SFTPA1 | ENST00000429958.5 | c.292+45del | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.208 AC: 31516AN: 151866Hom.: 3532 Cov.: 26
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GnomAD3 exomes AF: 0.231 AC: 57731AN: 249618Hom.: 7482 AF XY: 0.240 AC XY: 32382AN XY: 135008
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GnomAD4 exome AF: 0.207 AC: 301173AN: 1456522Hom.: 34155 Cov.: 30 AF XY: 0.212 AC XY: 153757AN XY: 724640
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GnomAD4 genome ? AF: 0.208 AC: 31557AN: 151982Hom.: 3539 Cov.: 26 AF XY: 0.211 AC XY: 15668AN XY: 74278
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at