10-79946525-A-G
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_003019.5(SFTPD):c.135T>C(p.Ser45Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0619 in 1,613,760 control chromosomes in the GnomAD database, including 3,521 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_003019.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SFTPD | NM_003019.5 | c.135T>C | p.Ser45Ser | synonymous_variant | Exon 2 of 8 | ENST00000372292.8 | NP_003010.4 | |
SFTPD | XM_011540087.2 | c.135T>C | p.Ser45Ser | synonymous_variant | Exon 2 of 8 | XP_011538389.1 | ||
SFTPD | XM_011540088.3 | c.135T>C | p.Ser45Ser | synonymous_variant | Exon 2 of 7 | XP_011538390.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SFTPD | ENST00000372292.8 | c.135T>C | p.Ser45Ser | synonymous_variant | Exon 2 of 8 | 1 | NM_003019.5 | ENSP00000361366.3 | ||
SFTPD | ENST00000444384.3 | c.174T>C | p.Ser58Ser | synonymous_variant | Exon 2 of 6 | 3 | ENSP00000394325.1 | |||
ENSG00000283913 | ENST00000421889.1 | n.334-3503A>G | intron_variant | Intron 3 of 3 | 3 | |||||
ENSG00000283913 | ENST00000453174.7 | n.962-3503A>G | intron_variant | Intron 7 of 7 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0479 AC: 7278AN: 151892Hom.: 239 Cov.: 33
GnomAD3 exomes AF: 0.0462 AC: 11604AN: 251372Hom.: 381 AF XY: 0.0458 AC XY: 6222AN XY: 135872
GnomAD4 exome AF: 0.0634 AC: 92658AN: 1461750Hom.: 3282 Cov.: 32 AF XY: 0.0622 AC XY: 45200AN XY: 727186
GnomAD4 genome AF: 0.0479 AC: 7274AN: 152010Hom.: 239 Cov.: 33 AF XY: 0.0445 AC XY: 3308AN XY: 74316
ClinVar
Submissions by phenotype
not specified Benign:1
Ser45Ser in exon 2 of SFTPD: This variant is not expected to have clinical signi ficance because it does not alter an amino acid residue and is not located withi n the splice consensus sequence. It has been identified in 6.8% (589/8600) of Eu ropean American chromosomes from a broad population by the NHLBI Exome Sequencin g Project (http://evs.gs.washington.edu/EVS; dbSNP rs6413520). -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at