10-79938155-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_003019.5(SFTPD):c.825G>A(p.Thr275Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000746 in 1,610,670 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_003019.5 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 |
---|---|---|---|---|---|---|---|---|
SFTPD | NM_003019.5 | c.825G>A | p.Thr275Thr | synonymous_variant | Exon 8 of 8 | ENST00000372292.8 | NP_003010.4 | |
SFTPD | XM_011540087.2 | c.825G>A | p.Thr275Thr | synonymous_variant | Exon 8 of 8 | XP_011538389.1 | ||
SFTPD | XM_011540088.3 | c.708G>A | p.Thr236Thr | synonymous_variant | Exon 7 of 7 | XP_011538390.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000388 AC: 59AN: 152162Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00156 AC: 392AN: 251248Hom.: 5 AF XY: 0.00208 AC XY: 282AN XY: 135778
GnomAD4 exome AF: 0.000783 AC: 1142AN: 1458390Hom.: 19 Cov.: 32 AF XY: 0.00111 AC XY: 806AN XY: 724648
GnomAD4 genome AF: 0.000387 AC: 59AN: 152280Hom.: 1 Cov.: 32 AF XY: 0.000564 AC XY: 42AN XY: 74446
ClinVar
Submissions by phenotype
SFTPD-related disorder Benign:1
This variant is classified as 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