18-63902432-A-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_002575.3(SERPINB2):ā€‹c.707A>Gā€‹(p.Tyr236Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,460,956 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: not found (cov: 33)
Exomes š‘“: 0.0000014 ( 0 hom. )

Consequence

SERPINB2
NM_002575.3 missense

Scores

1
4
14

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.815
Variant links:
Genes affected
SERPINB2 (HGNC:8584): (serpin family B member 2) Predicted to enable serine-type endopeptidase inhibitor activity. Predicted to be involved in negative regulation of endopeptidase activity. Predicted to be located in extracellular region and plasma membrane. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.20606586).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SERPINB2NM_002575.3 linkc.707A>G p.Tyr236Cys missense_variant Exon 7 of 8 ENST00000299502.9 NP_002566.1 P05120
SERPINB2NM_001143818.2 linkc.707A>G p.Tyr236Cys missense_variant Exon 8 of 9 NP_001137290.1 P05120
SERPINB2XM_024451192.2 linkc.707A>G p.Tyr236Cys missense_variant Exon 7 of 8 XP_024306960.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SERPINB2ENST00000299502.9 linkc.707A>G p.Tyr236Cys missense_variant Exon 7 of 8 1 NM_002575.3 ENSP00000299502.4 P05120
ENSG00000289724ENST00000397996.6 linkc.335A>G p.Tyr112Cys missense_variant Exon 4 of 8 5 ENSP00000381082.2 H7BYS2

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000137
AC:
2
AN:
1460956
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
726770
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000180
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Apr 12, 2023
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.707A>G (p.Y236C) alteration is located in exon 8 (coding exon 6) of the SERPINB2 gene. This alteration results from a A to G substitution at nucleotide position 707, causing the tyrosine (Y) at amino acid position 236 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Benign
-0.17
T
BayesDel_noAF
Benign
-0.48
CADD
Benign
16
DANN
Benign
0.97
DEOGEN2
Uncertain
0.47
T;T
Eigen
Benign
-0.91
Eigen_PC
Benign
-1.0
FATHMM_MKL
Benign
0.31
N
LIST_S2
Benign
0.20
.;T
M_CAP
Benign
0.013
T
MetaRNN
Benign
0.21
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Uncertain
2.3
M;M
PrimateAI
Benign
0.34
T
PROVEAN
Pathogenic
-6.2
D;D
REVEL
Benign
0.15
Sift
Uncertain
0.0060
D;D
Sift4G
Uncertain
0.048
D;D
Polyphen
0.13
B;B
Vest4
0.23
MutPred
0.58
Gain of catalytic residue at M234 (P = 8e-04);Gain of catalytic residue at M234 (P = 8e-04);
MVP
0.13
MPC
0.019
ClinPred
0.79
D
GERP RS
-0.33
Varity_R
0.38
gMVP
0.46

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr18-61569666; API