rs1395267

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001370475.1(SERPINB11):​c.907T>A​(p.Ser303Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/17 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: 𝑓 0.0 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

SERPINB11
NM_001370475.1 missense

Scores

15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.427
Variant links:
Genes affected
SERPINB11 (HGNC:14221): (serpin family B member 11) Predicted to enable serine-type endopeptidase inhibitor activity. Predicted to be involved in negative regulation of endopeptidase activity. Predicted to be located in cytoplasm. 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 Likely_benign. Variant got -2 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.11618286).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SERPINB11NM_001370475.1 linkuse as main transcriptc.907T>A p.Ser303Thr missense_variant 8/8 ENST00000544088.6 NP_001357404.1
SERPINB11NM_080475.5 linkuse as main transcriptc.907T>A p.Ser303Thr missense_variant 9/9 NP_536723.2 Q96P15F5GYW9A9UKE9
SERPINB11NM_001291278.2 linkuse as main transcriptc.646T>A p.Ser216Thr missense_variant 6/6 NP_001278207.1 Q96P15A0A096LPD5A9UKE9
SERPINB11NM_001291279.2 linkuse as main transcriptc.382T>A p.Ser128Thr missense_variant 7/7 NP_001278208.1 B4DKT7A9UKE9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SERPINB11ENST00000544088.6 linkuse as main transcriptc.907T>A p.Ser303Thr missense_variant 8/82 NM_001370475.1 ENSP00000441497.1 F5GYW9

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
151970
Hom.:
0
Cov.:
31
FAILED QC
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1455646
Hom.:
0
Cov.:
50
AF XY:
0.00
AC XY:
0
AN XY:
723538
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:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
151970
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
74208
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.036
T
BayesDel_noAF
Benign
-0.29
CADD
Benign
15
DANN
Benign
0.71
Eigen
Benign
-0.77
Eigen_PC
Benign
-0.73
FATHMM_MKL
Benign
0.046
N
LIST_S2
Benign
0.10
.;T;T;T
M_CAP
Benign
0.017
T
MetaRNN
Benign
0.12
T;T;T;T
MetaSVM
Benign
-0.64
T
PrimateAI
Benign
0.32
T
PROVEAN
Benign
-0.92
.;N;.;.
REVEL
Benign
0.022
Sift4G
Benign
0.20
T;T;T;T
Vest4
0.091
MVP
0.20
MPC
0.013
ClinPred
0.18
T
GERP RS
2.3
gMVP
0.23

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1395267; hg19: chr18-61390361; API