chr18-63658582-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_006919.3(SERPINB3):c.400G>A(p.Val134Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0114 in 1,591,476 control chromosomes in the GnomAD database, including 291 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V134A) has been classified as Likely benign.
Frequency
Consequence
NM_006919.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERPINB3 | NM_006919.3 | c.400G>A | p.Val134Ile | missense_variant | 5/8 | ENST00000283752.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERPINB3 | ENST00000283752.10 | c.400G>A | p.Val134Ile | missense_variant | 5/8 | 1 | NM_006919.3 | P1 | |
SERPINB3 | ENST00000332821.8 | c.400G>A | p.Val134Ile | missense_variant | 5/7 | 1 | |||
SERPINB11 | ENST00000489748.5 | c.-16+2606C>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00969 AC: 1465AN: 151140Hom.: 15 Cov.: 31
GnomAD3 exomes AF: 0.00175 AC: 437AN: 250402Hom.: 2 AF XY: 0.00182 AC XY: 246AN XY: 135376
GnomAD4 exome AF: 0.0115 AC: 16619AN: 1440218Hom.: 276 Cov.: 30 AF XY: 0.0113 AC XY: 8104AN XY: 716956
GnomAD4 genome AF: 0.00969 AC: 1465AN: 151258Hom.: 15 Cov.: 31 AF XY: 0.00895 AC XY: 662AN XY: 73962
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2024 | SERPINB3: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at