chr10-79557350-A-G
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001098668.4(SFTPA2):c.606T>C(p.Asp202=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00374 in 150,796 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0037 ( 1 hom., cov: 31)
Exomes 𝑓: 0.0012 ( 11 hom. )
Failed GnomAD Quality Control
Consequence
SFTPA2
NM_001098668.4 synonymous
NM_001098668.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.231
Genes affected
SFTPA2 (HGNC:10799): (surfactant protein A2) This gene is one of several genes encoding pulmonary-surfactant associated proteins (SFTPA) located on chromosome 10. Mutations in this gene and a highly similar gene located nearby, which affect the highly conserved carbohydrate recognition domain, are associated with idiopathic pulmonary fibrosis. The current version of the assembly displays only a single centromeric SFTPA gene pair rather than the two gene pairs shown in the previous assembly which were thought to have resulted from a duplication. [provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BP6
?
Variant 10-79557350-A-G is Benign according to our data. Variant chr10-79557350-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2640641.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.231 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00374 (564/150796) while in subpopulation AFR AF= 0.00579 (238/41108). AF 95% confidence interval is 0.00519. There are 1 homozygotes in gnomad4. There are 265 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High AC in GnomAd at 556 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SFTPA2 | NM_001098668.4 | c.606T>C | p.Asp202= | synonymous_variant | 6/6 | ENST00000372325.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SFTPA2 | ENST00000372325.7 | c.606T>C | p.Asp202= | synonymous_variant | 6/6 | 1 | NM_001098668.4 | P1 | |
SFTPA2 | ENST00000372327.9 | c.606T>C | p.Asp202= | synonymous_variant | 5/5 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00369 AC: 556AN: 150676Hom.: 1 Cov.: 31
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GnomAD3 exomes AF: 0.000786 AC: 197AN: 250760Hom.: 4 AF XY: 0.000686 AC XY: 93AN XY: 135556
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00120 AC: 1751AN: 1454642Hom.: 11 Cov.: 34 AF XY: 0.00120 AC XY: 870AN XY: 723826
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Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome ? AF: 0.00374 AC: 564AN: 150796Hom.: 1 Cov.: 31 AF XY: 0.00359 AC XY: 265AN XY: 73860
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | SFTPA2: BP4, BP7, BS2 - |
Computational scores
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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