GeneBe

2-218881037-C-A

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7

The NM_025216.3(WNT10A):​c.42C>A​(p.Pro14Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000069 in 1,450,010 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )

Consequence

WNT10A
NM_025216.3 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.626
Variant links:
Genes affected
WNT10A (HGNC:13829): (Wnt family member 10A) The WNT gene family consists of structurally related genes which encode secreted signaling proteins. These proteins have been implicated in oncogenesis and in several developmental processes, including regulation of cell fate and patterning during embryogenesis. This gene is a member of the WNT gene family. It is strongly expressed in the cell lines of promyelocytic leukemia and Burkitt's lymphoma. In addition, it and another family member, the WNT6 gene, are strongly coexpressed in colorectal cancer cell lines. The gene overexpression may play key roles in carcinogenesis through activation of the WNT-beta-catenin-TCF signaling pathway. This gene and the WNT6 gene are clustered in the chromosome 2q35 region. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BP6
Variant 2-218881037-C-A is Benign according to our data. Variant chr2-218881037-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 1621817.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.626 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
WNT10ANM_025216.3 linkc.42C>A p.Pro14Pro synonymous_variant Exon 1 of 4 ENST00000258411.8 NP_079492.2 Q9GZT5A0A2K8FR47
WNT10AXM_011511930.2 linkc.42C>A p.Pro14Pro synonymous_variant Exon 1 of 3 XP_011510232.1
WNT10AXM_011511929.3 linkc.18-1124C>A intron_variant Intron 2 of 4 XP_011510231.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
WNT10AENST00000258411.8 linkc.42C>A p.Pro14Pro synonymous_variant Exon 1 of 4 1 NM_025216.3 ENSP00000258411.3 Q9GZT5
ENSG00000300702ENST00000773519.1 linkn.*189C>A downstream_gene_variant

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
6.90e-7
AC:
1
AN:
1450010
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
720130
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
33298
American (AMR)
AF:
0.00
AC:
0
AN:
43718
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25892
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39280
South Asian (SAS)
AF:
0.00
AC:
0
AN:
84252
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
51154
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5756
European-Non Finnish (NFE)
AF:
9.03e-7
AC:
1
AN:
1106830
Other (OTH)
AF:
0.00
AC:
0
AN:
59830
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00
Hom.:
0
Bravo
AF:
0.00000756

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Odonto-onycho-dermal dysplasia;C1835492:Tooth agenesis, selective, 4 Benign:1
Apr 26, 2023
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.43
CADD
Benign
9.1
DANN
Benign
0.92
PhyloP100
-0.63
PromoterAI
0.029
Neutral
Mutation Taster
=100/0
polymorphism

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 for variant 2:218881037 C>A . It may be empty.

Other links and lift over

dbSNP: rs1168115806; hg19: chr2-219745759; API