chr10-79612416-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_005411.5(SFTPA1):c.277G>A(p.Glu93Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000106 in 1,613,666 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
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.277G>A | p.Glu93Lys | missense_variant | 4/6 | ENST00000398636.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SFTPA1 | ENST00000398636.8 | c.277G>A | p.Glu93Lys | missense_variant | 4/6 | 1 | NM_005411.5 | P1 | |
SFTPA1 | ENST00000419470.6 | c.322G>A | p.Glu108Lys | missense_variant | 4/6 | 1 | |||
SFTPA1 | ENST00000428376.6 | c.277G>A | p.Glu93Lys | missense_variant | 3/5 | 1 | P1 | ||
SFTPA1 | ENST00000429958.5 | c.277G>A | p.Glu93Lys | missense_variant | 3/5 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000921 AC: 14AN: 152036Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251304Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135830
GnomAD4 exome AF: 0.000107 AC: 157AN: 1461512Hom.: 0 Cov.: 34 AF XY: 0.000100 AC XY: 73AN XY: 727064
GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74390
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 23, 2023 | The c.277G>A (p.E93K) alteration is located in exon 4 (coding exon 2) of the SFTPA1 gene. This alteration results from a G to A substitution at nucleotide position 277, causing the glutamic acid (E) at amino acid position 93 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at