rs1998374
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003019.5(SFTPD):c.200-87A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 838,808 control chromosomes in the GnomAD database, including 14,320 homozygotes. 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 0.18 ( 3221 hom., cov: 32)
Exomes 𝑓: 0.15 ( 11099 hom. )
Consequence
SFTPD
NM_003019.5 intron
NM_003019.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.596
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SFTPD | NM_003019.5 | c.200-87A>G | intron_variant | ENST00000372292.8 | |||
SFTPD | XM_011540087.2 | c.200-87A>G | intron_variant | ||||
SFTPD | XM_011540088.3 | c.200-87A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SFTPD | ENST00000372292.8 | c.200-87A>G | intron_variant | 1 | NM_003019.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.182 AC: 27613AN: 151948Hom.: 3208 Cov.: 32
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GnomAD4 exome AF: 0.151 AC: 103807AN: 686742Hom.: 11099 AF XY: 0.155 AC XY: 56681AN XY: 366614
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GnomAD4 genome ? AF: 0.182 AC: 27675AN: 152066Hom.: 3221 Cov.: 32 AF XY: 0.185 AC XY: 13782AN XY: 74342
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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