20-45512743-C-G

Variant summary

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

The NM_006652.2(SPINT3):​c.178G>C​(p.Glu60Gln) 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. 15/19 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)

Consequence

SPINT3
NM_006652.2 missense

Scores

1
17

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.762
Variant links:
Genes affected
SPINT3 (HGNC:11248): (serine peptidase inhibitor, Kunitz type 3) Predicted to enable receptor antagonist activity and transforming growth factor beta binding activity. Predicted to be involved in negative regulation of transforming growth factor beta receptor signaling pathway. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

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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=0.08064523).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SPINT3NM_006652.2 linkc.178G>C p.Glu60Gln missense_variant Exon 2 of 2 ENST00000217428.7 NP_006643.1 P49223
LOC107987282XR_001754641.3 linkn.100-20531C>G intron_variant Intron 1 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SPINT3ENST00000217428.7 linkc.178G>C p.Glu60Gln missense_variant Exon 2 of 2 1 NM_006652.2 ENSP00000217428.6 P49223

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
33
GnomAD4 genome
Cov.:
32

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Dec 24, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.178G>C (p.E60Q) alteration is located in exon 2 (coding exon 2) of the SPINT3 gene. This alteration results from a G to C substitution at nucleotide position 178, causing the glutamic acid (E) at amino acid position 60 to be replaced by a glutamine (Q). 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
-0.22
T
BayesDel_noAF
Benign
-0.56
CADD
Benign
0.16
DANN
Benign
0.35
DEOGEN2
Benign
0.0012
T
Eigen
Benign
-1.3
Eigen_PC
Benign
-1.4
FATHMM_MKL
Benign
0.024
N
LIST_S2
Uncertain
0.88
D
M_CAP
Benign
0.0053
T
MetaRNN
Benign
0.081
T
MetaSVM
Benign
-0.91
T
PrimateAI
Benign
0.23
T
PROVEAN
Benign
0.16
N
REVEL
Benign
0.026
Sift
Benign
0.17
T
Sift4G
Benign
0.32
T
Polyphen
0.13
B
Vest4
0.091
MutPred
0.39
Gain of catalytic residue at C61 (P = 0.1542);
MVP
0.092
ClinPred
0.15
T
GERP RS
-2.7
Varity_R
0.048
gMVP
0.50

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: chr20-44141383; API