10-79611960-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_005411.5(SFTPA1):c.135C>T(p.Asp45Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000332 in 1,613,684 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_005411.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SFTPA1 | NM_005411.5 | c.135C>T | p.Asp45Asp | synonymous_variant | Exon 3 of 6 | ENST00000398636.8 | NP_005402.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SFTPA1 | ENST00000398636.8 | c.135C>T | p.Asp45Asp | synonymous_variant | Exon 3 of 6 | 1 | NM_005411.5 | ENSP00000381633.3 | ||
SFTPA1 | ENST00000419470.6 | c.180C>T | p.Asp60Asp | synonymous_variant | Exon 3 of 6 | 1 | ENSP00000397082.2 | |||
SFTPA1 | ENST00000428376.6 | c.135C>T | p.Asp45Asp | synonymous_variant | Exon 2 of 5 | 1 | ENSP00000411102.2 | |||
SFTPA1 | ENST00000429958.5 | c.135C>T | p.Asp45Asp | synonymous_variant | Exon 2 of 5 | 1 | ENSP00000395527.1 |
Frequencies
GnomAD3 genomes AF: 0.000454 AC: 69AN: 151984Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000734 AC: 184AN: 250682Hom.: 1 AF XY: 0.000760 AC XY: 103AN XY: 135516
GnomAD4 exome AF: 0.000320 AC: 467AN: 1461582Hom.: 4 Cov.: 92 AF XY: 0.000322 AC XY: 234AN XY: 727100
GnomAD4 genome AF: 0.000454 AC: 69AN: 152102Hom.: 0 Cov.: 32 AF XY: 0.000619 AC XY: 46AN XY: 74364
ClinVar
Submissions by phenotype
SFTPA1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at