20-45515547-G-A

Variant summary

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

The NM_006652.2(SPINT3):​c.62C>T​(p.Ser21Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000022 in 1,548,790 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0000067 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000024 ( 0 hom. )

Consequence

SPINT3
NM_006652.2 missense

Scores

2
16

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.300
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]

Genome browser will be placed here

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=0.07664806).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SPINT3NM_006652.2 linkc.62C>T p.Ser21Leu missense_variant Exon 1 of 2 ENST00000217428.7 NP_006643.1 P49223
LOC107987282XR_001754641.3 linkn.100-17727G>A intron_variant Intron 1 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SPINT3ENST00000217428.7 linkc.62C>T p.Ser21Leu missense_variant Exon 1 of 2 1 NM_006652.2 ENSP00000217428.6 P49223

Frequencies

GnomAD3 genomes
AF:
0.00000668
AC:
1
AN:
149744
Hom.:
0
Cov.:
31
show subpopulations
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:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000236
AC:
33
AN:
1398932
Hom.:
0
Cov.:
32
AF XY:
0.0000232
AC XY:
16
AN XY:
689980
show subpopulations
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:
0.0000287
Gnomad4 OTH exome
AF:
0.0000345
GnomAD4 genome
AF:
0.00000667
AC:
1
AN:
149858
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
72956
show subpopulations
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:
0.0000147
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000302

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Oct 16, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.62C>T (p.S21L) alteration is located in exon 1 (coding exon 1) of the SPINT3 gene. This alteration results from a C to T substitution at nucleotide position 62, causing the serine (S) at amino acid position 21 to be replaced by a leucine (L). 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
0.18
BayesDel_addAF
Benign
-0.15
T
BayesDel_noAF
Benign
-0.46
CADD
Benign
17
DANN
Uncertain
0.98
DEOGEN2
Benign
0.0044
T
Eigen
Benign
-0.77
Eigen_PC
Benign
-0.90
FATHMM_MKL
Benign
0.069
N
LIST_S2
Benign
0.56
T
M_CAP
Benign
0.010
T
MetaRNN
Benign
0.077
T
MetaSVM
Benign
-1.1
T
PrimateAI
Benign
0.35
T
PROVEAN
Benign
-1.2
N
REVEL
Benign
0.025
Sift
Uncertain
0.014
D
Sift4G
Benign
0.14
T
Polyphen
0.45
B
Vest4
0.19
MVP
0.25
ClinPred
0.15
T
GERP RS
0.15
Varity_R
0.083
gMVP
0.49

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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: rs151265860; hg19: chr20-44144187; COSMIC: COSV54156153; API