GeneBe

rs6104

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_002575.3(SERPINB2):​c.1238C>A​(p.Ser413Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

SERPINB2
NM_002575.3 missense

Scores

3
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.933

Publications

46 publications found
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]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.09064734).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002575.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
SERPINB2
NM_002575.3
MANE Select
c.1238C>Ap.Ser413Tyr
missense
Exon 8 of 8NP_002566.1P05120
SERPINB2
NM_001143818.2
c.1238C>Ap.Ser413Tyr
missense
Exon 9 of 9NP_001137290.1P05120

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
SERPINB2
ENST00000299502.9
TSL:1 MANE Select
c.1238C>Ap.Ser413Tyr
missense
Exon 8 of 8ENSP00000299502.4P05120
ENSG00000289724
ENST00000418725.1
TSL:5
c.546+320C>A
intron
N/AENSP00000392381.1H7C004
SERPINB2
ENST00000457692.5
TSL:5
c.1238C>Ap.Ser413Tyr
missense
Exon 9 of 9ENSP00000401645.1P05120

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1376336
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
675540
African (AFR)
AF:
0.00
AC:
0
AN:
30520
American (AMR)
AF:
0.00
AC:
0
AN:
31784
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
20844
East Asian (EAS)
AF:
0.00
AC:
0
AN:
38624
South Asian (SAS)
AF:
0.00
AC:
0
AN:
71584
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
50602
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5346
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1070350
Other (OTH)
AF:
0.00
AC:
0
AN:
56682
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00
Hom.:
2480

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.16
BayesDel_addAF
Benign
-0.060
T
BayesDel_noAF
Benign
-0.32
CADD
Benign
17
DANN
Uncertain
0.98
DEOGEN2
Benign
0.34
T
Eigen
Benign
-0.71
Eigen_PC
Benign
-0.75
FATHMM_MKL
Benign
0.31
N
LIST_S2
Benign
0.85
T
M_CAP
Benign
0.060
D
MetaRNN
Benign
0.091
T
MetaSVM
Benign
-0.57
T
MutationAssessor
Uncertain
2.2
M
PhyloP100
0.93
PrimateAI
Benign
0.28
T
PROVEAN
Uncertain
-2.4
N
REVEL
Benign
0.12
Sift
Benign
0.071
T
Sift4G
Benign
0.19
T
Polyphen
0.080
B
Vest4
0.14
MutPred
0.28
Loss of disorder (P = 0.0182)
MVP
0.58
MPC
0.092
ClinPred
0.51
D
GERP RS
1.3
Varity_R
0.32
gMVP
0.19
Mutation Taster
=97/3
polymorphism

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

Other links and lift over

dbSNP: rs6104; hg19: chr18-61570529; API