rs1059046
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001098668.4(SFTPA2):āc.26C>Gā(p.Thr9Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000312 in 1,602,498 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T9N) has been classified as Benign.
Frequency
Consequence
NM_001098668.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SFTPA2 | NM_001098668.4 | c.26C>G | p.Thr9Ser | missense_variant | 3/6 | ENST00000372325.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SFTPA2 | ENST00000372325.7 | c.26C>G | p.Thr9Ser | missense_variant | 3/6 | 1 | NM_001098668.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000200 AC: 3AN: 150306Hom.: 0 Cov.: 27
GnomAD3 exomes AF: 0.0000215 AC: 4AN: 185672Hom.: 0 AF XY: 0.0000202 AC XY: 2AN XY: 99180
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1452074Hom.: 0 Cov.: 79 AF XY: 0.00000138 AC XY: 1AN XY: 722292
GnomAD4 genome ? AF: 0.0000199 AC: 3AN: 150424Hom.: 0 Cov.: 27 AF XY: 0.0000273 AC XY: 2AN XY: 73362
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at