rs139899873
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_005411.5(SFTPA1):āc.26A>Cā(p.Asn9Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00155 in 1,613,692 control chromosomes in the GnomAD database, including 44 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_005411.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SFTPA1 | NM_005411.5 | c.26A>C | p.Asn9Thr | missense_variant | 3/6 | ENST00000398636.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SFTPA1 | ENST00000398636.8 | c.26A>C | p.Asn9Thr | missense_variant | 3/6 | 1 | NM_005411.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00825 AC: 1255AN: 152094Hom.: 23 Cov.: 34
GnomAD3 exomes AF: 0.00121 AC: 304AN: 250754Hom.: 3 AF XY: 0.000885 AC XY: 120AN XY: 135592
GnomAD4 exome AF: 0.000850 AC: 1242AN: 1461482Hom.: 19 Cov.: 124 AF XY: 0.000722 AC XY: 525AN XY: 727060
GnomAD4 genome AF: 0.00827 AC: 1259AN: 152210Hom.: 25 Cov.: 34 AF XY: 0.00748 AC XY: 557AN XY: 74444
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Dec 16, 2015 | p.Asn24Thr in exon 3 of SFTPA1: This variant is not expected to have clinical si gnificance due to a lack of conservation across species, including mammals. Of n ote, >10 mammals have a threonine (Thr) at this position. In addition, computati onal prediction tools do not suggest a high likelihood of impact to the protein. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at