chr10-79612324-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_005411.5(SFTPA1):c.185C>T(p.Pro62Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00411 in 1,613,882 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P62P) has been classified as Benign.
Frequency
Consequence
NM_005411.5 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SFTPA1 | NM_005411.5 | c.185C>T | p.Pro62Leu | missense_variant | 4/6 | ENST00000398636.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SFTPA1 | ENST00000398636.8 | c.185C>T | p.Pro62Leu | missense_variant | 4/6 | 1 | NM_005411.5 | P1 | |
SFTPA1 | ENST00000419470.6 | c.230C>T | p.Pro77Leu | missense_variant | 4/6 | 1 | |||
SFTPA1 | ENST00000428376.6 | c.185C>T | p.Pro62Leu | missense_variant | 3/5 | 1 | P1 | ||
SFTPA1 | ENST00000429958.5 | c.185C>T | p.Pro62Leu | missense_variant | 3/5 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00288 AC: 438AN: 152110Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00265 AC: 666AN: 251464Hom.: 1 AF XY: 0.00266 AC XY: 361AN XY: 135904
GnomAD4 exome AF: 0.00424 AC: 6201AN: 1461656Hom.: 13 Cov.: 34 AF XY: 0.00411 AC XY: 2989AN XY: 727116
GnomAD4 genome ? AF: 0.00288 AC: 438AN: 152226Hom.: 2 Cov.: 32 AF XY: 0.00297 AC XY: 221AN XY: 74438
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at