rs2069990
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_000624.6(SERPINA5):c.*38G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0242 in 1,585,086 control chromosomes in the GnomAD database, including 549 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 0.022 ( 38 hom., cov: 33)
Exomes 𝑓: 0.024 ( 511 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: 0.799
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=-0.82).
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0222 (3378/152310) while in subpopulation SAS AF= 0.0321 (155/4828). AF 95% confidence interval is 0.028. There are 38 homozygotes in gnomad4. There are 1706 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 38 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERPINA5 | NM_000624.6 | c.*38G>A | 3_prime_UTR_variant | 6/6 | ENST00000329597.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERPINA5 | ENST00000329597.12 | c.*38G>A | 3_prime_UTR_variant | 6/6 | 1 | NM_000624.6 | P1 | ||
SERPINA5 | ENST00000554276.1 | c.*38G>A | 3_prime_UTR_variant | 5/5 | 1 | P1 | |||
SERPINA5 | ENST00000553780.5 | c.*38G>A | 3_prime_UTR_variant | 7/7 | 5 | P1 | |||
SERPINA5 | ENST00000554866.5 | c.*38G>A | 3_prime_UTR_variant | 5/5 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0222 AC: 3376AN: 152192Hom.: 38 Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0267 AC: 6108AN: 229152Hom.: 100 AF XY: 0.0280 AC XY: 3444AN XY: 123072
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GnomAD4 exome AF: 0.0244 AC: 34996AN: 1432776Hom.: 511 Cov.: 31 AF XY: 0.0253 AC XY: 17939AN XY: 709946
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GnomAD4 genome ? AF: 0.0222 AC: 3378AN: 152310Hom.: 38 Cov.: 33 AF XY: 0.0229 AC XY: 1706AN XY: 74482
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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