chr10-79557444-T-A
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM2PM5PP3_StrongPP5
The NM_001098668.4(SFTPA2):c.512A>T(p.Asn171Ile) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N171Y) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001098668.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SFTPA2 | NM_001098668.4 | c.512A>T | p.Asn171Ile | missense_variant | 6/6 | ENST00000372325.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SFTPA2 | ENST00000372325.7 | c.512A>T | p.Asn171Ile | missense_variant | 6/6 | 1 | NM_001098668.4 | P1 | |
SFTPA2 | ENST00000372327.9 | c.512A>T | p.Asn171Ile | missense_variant | 5/5 | 1 | P1 | ||
SFTPA2 | ENST00000417041.1 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome Cov.: 34
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
Interstitial lung disease 2 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 18, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.