chr12-130163401-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4BP7

The NM_007197.4(FZD10):​c.459C>T​(p.Asn153Asn) variant causes a synonymous 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)

Consequence

FZD10
NM_007197.4 synonymous

Scores

1
2
10

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.54
Variant links:
Genes affected
FZD10 (HGNC:4039): (frizzled class receptor 10) This gene is a member of the frizzled gene family. Members of this family encode 7-transmembrane domain proteins that are receptors for the Wingless type MMTV integration site family of signaling proteins. Most frizzled receptors are coupled to the beta-catenin canonical signaling pathway. Using array analysis, expression of this intronless gene is significantly up-regulated in two cases of primary colon cancer. [provided by RefSeq, Jul 2008]

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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=0.26718256).
BP7
Synonymous conserved (PhyloP=1.54 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FZD10NM_007197.4 linkc.459C>T p.Asn153Asn synonymous_variant Exon 1 of 1 ENST00000229030.5 NP_009128.1 Q9ULW2Q6NSL8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FZD10ENST00000229030.5 linkc.459C>T p.Asn153Asn synonymous_variant Exon 1 of 1 6 NM_007197.4 ENSP00000229030.4 Q9ULW2
FZD10ENST00000539839.1 linkc.361C>T p.Arg121Trp missense_variant Exon 1 of 1 6 ENSP00000438460.1 F5H450

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
35
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.16
T
BayesDel_noAF
Benign
-0.46
CADD
Benign
11
DANN
Benign
0.97
Eigen
Benign
0.17
Eigen_PC
Benign
0.21
FATHMM_MKL
Uncertain
0.92
D
M_CAP
Benign
0.011
T
MetaRNN
Benign
0.27
T
MetaSVM
Benign
-0.53
T
PROVEAN
Pathogenic
-8.0
D
REVEL
Benign
0.24
Sift4G
Uncertain
0.019
D
Vest4
0.33
MutPred
0.26
Gain of catalytic residue at R124 (P = 0.0016);
MVP
0.60
ClinPred
0.43
T
GERP RS
4.1

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. It may be empty.

Other links and lift over

dbSNP: rs766910008; hg19: chr12-130647946; COSMIC: COSV57472804; COSMIC: COSV57472804; API