rs8004738
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000355814.8(SERPINA1):c.-162C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 152,556 control chromosomes in the GnomAD database, including 23,234 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 0.54 ( 23168 hom., cov: 33)
Exomes 𝑓: 0.56 ( 66 hom. )
Consequence
SERPINA1
ENST00000355814.8 5_prime_UTR
ENST00000355814.8 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.07
Genes affected
SERPINA1 (HGNC:8941): (serpin family A member 1) The protein encoded by this gene is a serine protease inhibitor belonging to the serpin superfamily whose targets include elastase, plasmin, thrombin, trypsin, chymotrypsin, and plasminogen activator. This protein is produced in the liver, the bone marrow, by lymphocytic and monocytic cells in lymphoid tissue, and by the Paneth cells of the gut. Defects in this gene are associated with chronic obstructive pulmonary disease, emphysema, and chronic liver disease. Several transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Aug 2020]
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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=-0.79).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERPINA1 | NM_001002235.3 | c.-125C>T | 5_prime_UTR_variant | 1/5 | |||
SERPINA1 | NM_001002236.3 | c.-439C>T | 5_prime_UTR_variant | 1/7 | |||
SERPINA1 | NM_001127700.2 | c.-162C>T | 5_prime_UTR_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERPINA1 | ENST00000355814.8 | c.-162C>T | 5_prime_UTR_variant | 1/5 | 1 | P1 | |||
SERPINA1 | ENST00000393088.8 | c.-439C>T | 5_prime_UTR_variant | 1/7 | 1 | P1 | |||
SERPINA1 | ENST00000404814.8 | c.-226C>T | 5_prime_UTR_variant | 1/6 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.543 AC: 82488AN: 151992Hom.: 23132 Cov.: 33
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GnomAD4 exome AF: 0.561 AC: 250AN: 446Hom.: 66 Cov.: 0 AF XY: 0.558 AC XY: 203AN XY: 364
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GnomAD4 genome ? AF: 0.543 AC: 82582AN: 152110Hom.: 23168 Cov.: 33 AF XY: 0.540 AC XY: 40184AN XY: 74358
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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
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