12-130163332-C-T

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7

The NM_007197.4(FZD10):​c.390C>T​(p.Asp130Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,820 control chromosomes in the GnomAD database, with no homozygous occurrence. 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)
Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

FZD10
NM_007197.4 synonymous

Scores

5
8

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.933
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 Likely_benign. Variant got -1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.21233916).
BP7
Synonymous conserved (PhyloP=0.933 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FZD10NM_007197.4 linkc.390C>T p.Asp130Asp 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.390C>T p.Asp130Asp synonymous_variant Exon 1 of 1 6 NM_007197.4 ENSP00000229030.4 Q9ULW2
FZD10ENST00000539839.1 linkc.292C>T p.Leu98Phe missense_variant Exon 1 of 1 6 ENSP00000438460.1 F5H450

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
6.85e-7
AC:
1
AN:
1460820
Hom.:
0
Cov.:
35
AF XY:
0.00000138
AC XY:
1
AN XY:
726726
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:
8.99e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33
Asia WGS
AF:
0.000289
AC:
1
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.22
T
BayesDel_noAF
Benign
-0.55
CADD
Benign
13
DANN
Benign
0.96
Eigen
Uncertain
0.24
Eigen_PC
Uncertain
0.29
FATHMM_MKL
Uncertain
0.83
D
M_CAP
Benign
0.022
T
MetaRNN
Benign
0.21
T
MetaSVM
Uncertain
-0.072
T
PROVEAN
Uncertain
-4.0
D
REVEL
Benign
0.22
Sift4G
Benign
0.24
T
Vest4
0.27
MutPred
0.25
Gain of catalytic residue at R97 (P = 0.0026);
MVP
0.16
ClinPred
0.34
T
GERP RS
4.8

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: rs112917999; hg19: chr12-130647877; API