chr10-79938155-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_003019.5(SFTPD):c.825G>A(p.Thr275=) 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 (★).
Frequency
Genomes: 𝑓 0.00039 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00078 ( 19 hom. )
Consequence
SFTPD
NM_003019.5 synonymous
NM_003019.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.80
Genes affected
SFTPD (HGNC:10803): (surfactant protein D) The protein encoded by this gene is part of the innate immune response, protecting the lungs against inhaled microorganisms and chemicals. The encoded protein may also be involved in surfactant metabolism. [provided by RefSeq, Jul 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
?
Variant 10-79938155-C-T is Benign according to our data. Variant chr10-79938155-C-T is described in ClinVar as [Benign]. Clinvar id is 3049291.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-2.8 with no splicing effect.
BS2
?
High Homozygotes in GnomAdExome at 5 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SFTPD | NM_003019.5 | c.825G>A | p.Thr275= | synonymous_variant | 8/8 | ENST00000372292.8 | |
SFTPD | XM_011540087.2 | c.825G>A | p.Thr275= | synonymous_variant | 8/8 | ||
SFTPD | XM_011540088.3 | c.708G>A | p.Thr236= | synonymous_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SFTPD | ENST00000372292.8 | c.825G>A | p.Thr275= | synonymous_variant | 8/8 | 1 | NM_003019.5 | P1 | |
SFTPD | ENST00000678361.1 | n.3030G>A | non_coding_transcript_exon_variant | 4/4 | |||||
SFTPD | ENST00000679234.1 | n.2951G>A | non_coding_transcript_exon_variant | 5/5 | |||||
ENST00000421889.1 | n.234+1499C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000388 AC: 59AN: 152162Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00156 AC: 392AN: 251248Hom.: 5 AF XY: 0.00208 AC XY: 282AN XY: 135778
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GnomAD4 exome AF: 0.000783 AC: 1142AN: 1458390Hom.: 19 Cov.: 32 AF XY: 0.00111 AC XY: 806AN XY: 724648
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GnomAD4 genome ? AF: 0.000387 AC: 59AN: 152280Hom.: 1 Cov.: 32 AF XY: 0.000564 AC XY: 42AN XY: 74446
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
SFTPD-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 19, 2019 | 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
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at