10-79557357-T-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM1BP4BS2
The NM_001098668.4(SFTPA2):c.599A>T(p.Tyr200Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000917 in 1,613,970 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001098668.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SFTPA2 | NM_001098668.4 | c.599A>T | p.Tyr200Phe | missense_variant | 6/6 | ENST00000372325.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SFTPA2 | ENST00000372325.7 | c.599A>T | p.Tyr200Phe | missense_variant | 6/6 | 1 | NM_001098668.4 | P1 | |
SFTPA2 | ENST00000372327.9 | c.599A>T | p.Tyr200Phe | missense_variant | 5/5 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152116Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251468Hom.: 0 AF XY: 0.0000441 AC XY: 6AN XY: 135908
GnomAD4 exome AF: 0.0000985 AC: 144AN: 1461854Hom.: 0 Cov.: 34 AF XY: 0.0000743 AC XY: 54AN XY: 727230
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152116Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74306
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at