rs17423808
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000372325.7(SFTPA2):c.26C>A(p.Thr9Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 1,350,312 control chromosomes in the GnomAD database, including 280,757 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
ENST00000372325.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SFTPA2 | NM_001098668.4 | c.26C>A | p.Thr9Asn | missense_variant | 3/6 | ENST00000372325.7 | NP_001092138.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SFTPA2 | ENST00000372325.7 | c.26C>A | p.Thr9Asn | missense_variant | 3/6 | 1 | NM_001098668.4 | ENSP00000361400 | P1 |
Frequencies
GnomAD3 genomes AF: 0.523 AC: 77988AN: 149154Hom.: 21171 Cov.: 27
GnomAD3 exomes AF: 0.455 AC: 84524AN: 185672Hom.: 31716 AF XY: 0.451 AC XY: 44740AN XY: 99180
GnomAD4 exome AF: 0.611 AC: 733932AN: 1201044Hom.: 259587 Cov.: 79 AF XY: 0.604 AC XY: 363151AN XY: 600936
GnomAD4 genome AF: 0.523 AC: 77999AN: 149268Hom.: 21170 Cov.: 27 AF XY: 0.516 AC XY: 37536AN XY: 72740
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | This variant is associated with the following publications: (PMID: 24950659) - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 12, 2015 | p.Thr9Asn in exon 3 of SFTPA2: This variant is not expected to have clinical sig nificance it has been identified in 41% (22324/54314) of European chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP r s1059046). - |
SFTPA2-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 26, 2021 | 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
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at