rs2295766
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_004568.6(SERPINB6):c.457G>A(p.Gly153Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000903 in 1,614,204 control chromosomes in the GnomAD database, including 14 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 Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_004568.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERPINB6 | NM_004568.6 | c.457G>A | p.Gly153Ser | missense_variant | 5/7 | ENST00000380539.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERPINB6 | ENST00000380539.7 | c.457G>A | p.Gly153Ser | missense_variant | 5/7 | 3 | NM_004568.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00116 AC: 177AN: 152202Hom.: 1 Cov.: 34
GnomAD3 exomes AF: 0.00408 AC: 1025AN: 251480Hom.: 8 AF XY: 0.00308 AC XY: 418AN XY: 135912
GnomAD4 exome AF: 0.000876 AC: 1280AN: 1461884Hom.: 13 Cov.: 67 AF XY: 0.000729 AC XY: 530AN XY: 727238
GnomAD4 genome ? AF: 0.00117 AC: 178AN: 152320Hom.: 1 Cov.: 34 AF XY: 0.00113 AC XY: 84AN XY: 74490
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 19, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Aug 31, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 29, 2019 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | May 07, 2012 | Gly153Ser in Exon 06 of SERPINB6: This variant is not expected to have clinical significance because it has been identified in 5.0% (5/100) of chromosomes from a population in the dbSNP database (http://www.ncbi.nlm.nih.gov/projects/SNP; rs 2295766). - |
SERPINB6-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 25, 2019 | This variant is classified as 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