chr10-79937897-A-AT
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The ENST00000372292.8(SFTPD):c.1082_1083insA(p.Asn361LysfsTer2) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Consequence
SFTPD
ENST00000372292.8 frameshift
ENST00000372292.8 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.86
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 Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SFTPD | NM_003019.5 | c.1082_1083insA | p.Asn361LysfsTer2 | frameshift_variant | 8/8 | ENST00000372292.8 | NP_003010.4 | |
SFTPD | XM_011540087.2 | c.1082_1083insA | p.Asn361LysfsTer2 | frameshift_variant | 8/8 | XP_011538389.1 | ||
SFTPD | XM_011540088.3 | c.965_966insA | p.Asn322LysfsTer2 | frameshift_variant | 7/7 | XP_011538390.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SFTPD | ENST00000372292.8 | c.1082_1083insA | p.Asn361LysfsTer2 | frameshift_variant | 8/8 | 1 | NM_003019.5 | ENSP00000361366 | P1 | |
SFTPD | ENST00000678361.1 | n.3287_3288insA | non_coding_transcript_exon_variant | 4/4 | ||||||
SFTPD | ENST00000679234.1 | n.3208_3209insA | non_coding_transcript_exon_variant | 5/5 | ||||||
ENST00000421889.1 | n.234+1243dup | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
SFTPD-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 19, 2022 | The SFTPD c.1082dupA variant is predicted to result in a frameshift and premature protein termination (p.Asn361Lysfs*2). To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.