chr10-79557496-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 3P and 5B. PM1PP5BP4BS2
The NM_001098668.4(SFTPA2):c.460G>C(p.Ala154Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000186 in 1,613,490 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001098668.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SFTPA2 | NM_001098668.4 | c.460G>C | p.Ala154Pro | missense_variant | 6/6 | ENST00000372325.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SFTPA2 | ENST00000372325.7 | c.460G>C | p.Ala154Pro | missense_variant | 6/6 | 1 | NM_001098668.4 | P1 | |
SFTPA2 | ENST00000372327.9 | c.460G>C | p.Ala154Pro | missense_variant | 5/5 | 1 | P1 | ||
SFTPA2 | ENST00000417041.1 | c.460G>C | p.Ala154Pro | missense_variant | 6/6 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000132 AC: 20AN: 151938Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000481 AC: 12AN: 249298Hom.: 0 AF XY: 0.0000518 AC XY: 7AN XY: 135170
GnomAD4 exome AF: 0.000192 AC: 280AN: 1461434Hom.: 0 Cov.: 34 AF XY: 0.000182 AC XY: 132AN XY: 726980
GnomAD4 genome ? AF: 0.000132 AC: 20AN: 152056Hom.: 0 Cov.: 31 AF XY: 0.000135 AC XY: 10AN XY: 74330
ClinVar
Submissions by phenotype
Interstitial lung disease 2 Pathogenic:1
Likely pathogenic, criteria provided, single submitter | research | Alder lab, University of Pittsburgh | Feb 01, 2022 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | SFTPA2: PS3:Supporting, PS4:Supporting - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at