rs34212847
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1
The NM_054023.5(SCGB3A2):c.279G>A(p.Val93=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00942 in 1,613,824 control chromosomes in the GnomAD database, including 439 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 0.018 ( 56 hom., cov: 32)
Exomes 𝑓: 0.0085 ( 383 hom. )
Consequence
SCGB3A2
NM_054023.5 synonymous
NM_054023.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0700
Genes affected
SCGB3A2 (HGNC:18391): (secretoglobin family 3A member 2) The protein encoded by this gene is a secreted lung surfactant protein and a downstream target of thyroid transcription factor. A single nucleotide polymorphism in the promoter of this gene results in susceptibility to asthma.[provided by RefSeq, Mar 2010]
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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=-0.46).
BP7
?
Synonymous conserved (PhyloP=-0.07 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0682 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCGB3A2 | NM_054023.5 | c.279G>A | p.Val93= | synonymous_variant | 3/3 | ENST00000296694.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCGB3A2 | ENST00000296694.5 | c.279G>A | p.Val93= | synonymous_variant | 3/3 | 1 | NM_054023.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0181 AC: 2761AN: 152176Hom.: 56 Cov.: 32
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GnomAD3 exomes AF: 0.0151 AC: 3802AN: 251056Hom.: 110 AF XY: 0.0152 AC XY: 2059AN XY: 135672
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GnomAD4 exome AF: 0.00851 AC: 12431AN: 1461530Hom.: 383 Cov.: 30 AF XY: 0.00907 AC XY: 6598AN XY: 727058
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GnomAD4 genome ? AF: 0.0181 AC: 2764AN: 152294Hom.: 56 Cov.: 32 AF XY: 0.0185 AC XY: 1375AN XY: 74474
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at