rs1650233
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005411.5(SFTPA1):c.148C>A(p.Leu50Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 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. L50V) has been classified as Likely benign.
Frequency
Consequence
NM_005411.5 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 |
---|---|---|---|---|---|---|---|
SFTPA1 | NM_005411.5 | c.148C>A | p.Leu50Ile | missense_variant | 3/6 | ENST00000398636.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SFTPA1 | ENST00000398636.8 | c.148C>A | p.Leu50Ile | missense_variant | 3/6 | 1 | NM_005411.5 | P1 | |
SFTPA1 | ENST00000419470.6 | c.193C>A | p.Leu65Ile | missense_variant | 3/6 | 1 | |||
SFTPA1 | ENST00000428376.6 | c.148C>A | p.Leu50Ile | missense_variant | 2/5 | 1 | P1 | ||
SFTPA1 | ENST00000429958.5 | c.148C>A | p.Leu50Ile | missense_variant | 2/5 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 29
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1436616Hom.: 0 Cov.: 66 AF XY: 0.00 AC XY: 0AN XY: 715414
GnomAD4 genome ? Cov.: 29
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at