rs6413522
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003019.5(SFTPD):c.199+9G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000311 in 1,609,300 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 33)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
SFTPD
NM_003019.5 intron
NM_003019.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.563
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 Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SFTPD | NM_003019.5 | c.199+9G>C | intron_variant | Intron 2 of 7 | ENST00000372292.8 | NP_003010.4 | ||
SFTPD | XM_011540087.2 | c.199+9G>C | intron_variant | Intron 2 of 7 | XP_011538389.1 | |||
SFTPD | XM_011540088.3 | c.199+9G>C | intron_variant | Intron 2 of 6 | XP_011538390.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SFTPD | ENST00000372292.8 | c.199+9G>C | intron_variant | Intron 2 of 7 | 1 | NM_003019.5 | ENSP00000361366.3 | |||
SFTPD | ENST00000444384.3 | c.238+9G>C | intron_variant | Intron 2 of 5 | 3 | ENSP00000394325.1 | ||||
ENSG00000283913 | ENST00000421889.1 | n.334-3576C>G | intron_variant | Intron 3 of 3 | 3 | |||||
ENSG00000283913 | ENST00000453174.7 | n.962-3576C>G | intron_variant | Intron 7 of 7 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152230Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250220Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135344
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GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1457070Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 725120
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GnomAD4 genome AF: 0.0000263 AC: 4AN: 152230Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74366
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ClinVar
Not reported inComputational scores
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Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at