1-67425146-C-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_001018069.2(SERBP1):c.542G>T(p.Arg181Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000178 in 1,459,382 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.000018 ( 0 hom. )
Consequence
SERBP1
NM_001018069.2 missense
NM_001018069.2 missense
Scores
6
6
6
Clinical Significance
Conservation
PhyloP100: 7.78
Genes affected
SERBP1 (HGNC:17860): (SERPINE1 mRNA binding protein 1) Enables SUMO binding activity; mRNA 3'-UTR binding activity; and ribosome binding activity. Involved in PML body organization. Located in cytosol and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.768
BS2
?
High AC in GnomAdExome at 6 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERBP1 | NM_001018069.2 | c.542G>T | p.Arg181Leu | missense_variant | 3/8 | ENST00000361219.11 | |
SERBP1 | NM_001018067.2 | c.542G>T | p.Arg181Leu | missense_variant | 3/8 | ||
SERBP1 | NM_001018068.2 | c.542G>T | p.Arg181Leu | missense_variant | 3/8 | ||
SERBP1 | NM_015640.4 | c.542G>T | p.Arg181Leu | missense_variant | 3/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERBP1 | ENST00000361219.11 | c.542G>T | p.Arg181Leu | missense_variant | 3/8 | 1 | NM_001018069.2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250702Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135572
GnomAD3 exomes
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250702
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4
AN XY:
135572
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GnomAD4 exome AF: 0.0000178 AC: 26AN: 1459382Hom.: 0 Cov.: 32 AF XY: 0.0000179 AC XY: 13AN XY: 726000
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32
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726000
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
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ExAC
?
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AC:
2
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 18, 2023 | The c.542G>T (p.R181L) alteration is located in exon 3 (coding exon 3) of the SERBP1 gene. This alteration results from a G to T substitution at nucleotide position 542, causing the arginine (R) at amino acid position 181 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
D;T;D;T
M_CAP
Benign
T
MetaRNN
Pathogenic
D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Pathogenic
M;M;M;M
MutationTaster
Benign
D;D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
D;D;D;D
REVEL
Pathogenic
Sift
Benign
T;T;T;T
Sift4G
Benign
T;T;T;T
Polyphen
0.27, 0.081
.;B;B;.
Vest4
MutPred
Loss of methylation at R181 (P = 9e-04);Loss of methylation at R181 (P = 9e-04);Loss of methylation at R181 (P = 9e-04);Loss of methylation at R181 (P = 9e-04);
MVP
MPC
1.2
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at