rs140456610
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_002974.4(SERPINB4):c.603G>T(p.Trp201Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000138 in 1,448,320 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
SERPINB4
NM_002974.4 missense
NM_002974.4 missense
Scores
1
12
5
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.902
Genes affected
SERPINB4 (HGNC:10570): (serpin family B member 4) The protein encoded by this gene is a member of the serpin family of serine protease inhibitors. The encoded protein is highly expressed in many tumor cells and can inactivate granzyme M, an enzyme that kills tumor cells. This protein, along with serpin B3, can be processed into smaller fragments that aggregate to form an autoantigen in psoriasis, probably by causing chronic inflammation. [provided by RefSeq, Jan 2017]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| SERPINB4 | NM_002974.4 | c.603G>T | p.Trp201Cys | missense_variant | Exon 6 of 8 | ENST00000341074.10 | NP_002965.1 | |
| SERPINB4 | NM_175041.2 | c.603G>T | p.Trp201Cys | missense_variant | Exon 6 of 8 | NP_778206.1 | ||
| SERPINB4 | XM_011526138.2 | c.603G>T | p.Trp201Cys | missense_variant | Exon 6 of 8 | XP_011524440.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| SERPINB4 | ENST00000341074.10 | c.603G>T | p.Trp201Cys | missense_variant | Exon 6 of 8 | 1 | NM_002974.4 | ENSP00000343445.5 | ||
| SERPINB4 | ENST00000413673.5 | c.606G>T | p.Trp202Cys | missense_variant | Exon 5 of 7 | 1 | ENSP00000398645.1 | |||
| SERPINB4 | ENST00000436264.1 | c.474G>T | p.Trp158Cys | missense_variant | Exon 5 of 6 | 5 | ENSP00000399796.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248786Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134838
GnomAD3 exomes
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GnomAD4 exome AF: 0.00000138 AC: 2AN: 1448320Hom.: 0 Cov.: 29 AF XY: 0.00000277 AC XY: 2AN XY: 721366
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GnomAD4 genome
GnomAD4 genome
Cov.:
32
ExAC
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1
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Uncertain
T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Benign
N
LIST_S2
Uncertain
D;D
M_CAP
Benign
D
MetaRNN
Uncertain
D;D
MetaSVM
Uncertain
T
MutationAssessor
Uncertain
M;.
PROVEAN
Pathogenic
D;D
REVEL
Uncertain
Sift
Uncertain
D;D
Sift4G
Benign
T;.
Polyphen
D;.
Vest4
MutPred
Loss of MoRF binding (P = 0.0295);.;
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at