rs7070
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000624.6(SERPINA5):c.*805A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 151,948 control chromosomes in the GnomAD database, including 12,946 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 0.40 ( 12946 hom., cov: 32)
Exomes 𝑓: 0.50 ( 0 hom. )
Consequence
SERPINA5
NM_000624.6 3_prime_UTR
NM_000624.6 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.21
Genes affected
SERPINA5 (HGNC:8723): (serpin family A member 5) The protein encoded by this gene is a member of the serpin family of proteins, a group of proteins that inhibit serine proteases. This gene is one in a cluster of serpin genes located on the q arm of chromosome 14. This family member is a glycoprotein that can inhibit several serine proteases, including protein C and various plasminogen activators and kallikreins, and it thus plays diverse roles in hemostasis and thrombosis in multiple organs. [provided by RefSeq, Aug 2012]
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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=-0.9).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERPINA5 | NM_000624.6 | c.*805A>G | 3_prime_UTR_variant | 6/6 | ENST00000329597.12 | ||
LOC112268127 | XR_002957587.2 | n.2738T>C | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERPINA5 | ENST00000329597.12 | c.*805A>G | 3_prime_UTR_variant | 6/6 | 1 | NM_000624.6 | P1 | ||
SERPINA5 | ENST00000554276.1 | c.*805A>G | 3_prime_UTR_variant | 5/5 | 1 | P1 | |||
SERPINA5 | ENST00000554866.5 | c.*805A>G | 3_prime_UTR_variant | 5/5 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.396 AC: 60133AN: 151822Hom.: 12946 Cov.: 32
GnomAD3 genomes
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32
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GnomAD4 exome AF: 0.500 AC: 3AN: 6Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 2AN XY: 4
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GnomAD4 genome ? AF: 0.396 AC: 60142AN: 151942Hom.: 12946 Cov.: 32 AF XY: 0.394 AC XY: 29293AN XY: 74264
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at