chr14-94614436-T-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_001085.5(SERPINA3):c.-6T>C variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000231 in 1,613,122 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 (no stars).
Frequency
Consequence
NM_001085.5 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SERPINA3 | NM_001085.5 | c.-6T>C | 5_prime_UTR_premature_start_codon_gain_variant | Exon 2 of 5 | ENST00000393078.5 | NP_001076.2 | ||
SERPINA3 | NM_001085.5 | c.-6T>C | splice_region_variant | Exon 2 of 5 | ENST00000393078.5 | NP_001076.2 | ||
SERPINA3 | NM_001085.5 | c.-6T>C | 5_prime_UTR_variant | Exon 2 of 5 | ENST00000393078.5 | NP_001076.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SERPINA3 | ENST00000393078 | c.-6T>C | 5_prime_UTR_premature_start_codon_gain_variant | Exon 2 of 5 | 1 | NM_001085.5 | ENSP00000376793.3 | |||
SERPINA3 | ENST00000393078.5 | c.-6T>C | splice_region_variant | Exon 2 of 5 | 1 | NM_001085.5 | ENSP00000376793.3 | |||
SERPINA3 | ENST00000393078 | c.-6T>C | 5_prime_UTR_variant | Exon 2 of 5 | 1 | NM_001085.5 | ENSP00000376793.3 | |||
ENSG00000273259 | ENST00000553947.1 | n.*821T>C | splice_region_variant, non_coding_transcript_exon_variant | Exon 5 of 8 | 2 | ENSP00000452367.2 | ||||
ENSG00000273259 | ENST00000553947.1 | n.*821T>C | 3_prime_UTR_variant | Exon 5 of 8 | 2 | ENSP00000452367.2 |
Frequencies
GnomAD3 genomes AF: 0.00129 AC: 196AN: 151976Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.000284 AC: 71AN: 249840Hom.: 0 AF XY: 0.000185 AC XY: 25AN XY: 135090
GnomAD4 exome AF: 0.000120 AC: 176AN: 1461032Hom.: 0 Cov.: 29 AF XY: 0.000110 AC XY: 80AN XY: 726834
GnomAD4 genome AF: 0.00130 AC: 197AN: 152090Hom.: 1 Cov.: 31 AF XY: 0.00117 AC XY: 87AN XY: 74324
ClinVar
Submissions by phenotype
SERPINA3-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at