rs6948009

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003391.3(WNT2):​c.*1796A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,296 control chromosomes in the GnomAD database, including 1,380 homozygotes. 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: 𝑓 0.11 ( 1380 hom., cov: 33)

Consequence

WNT2
NM_003391.3 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.148
Variant links:
Genes affected
WNT2 (HGNC:12780): (Wnt family member 2) This gene is a member of the WNT gene family. 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. Alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
WNT2NM_003391.3 linkuse as main transcriptc.*1796A>G 3_prime_UTR_variant 5/5 ENST00000265441.8
WNT2NR_024047.2 linkuse as main transcriptn.2884A>G non_coding_transcript_exon_variant 5/5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
WNT2ENST00000265441.8 linkuse as main transcriptc.*1796A>G 3_prime_UTR_variant 5/51 NM_003391.3 P1
WNT2ENST00000647844.1 linkuse as main transcriptc.*2794A>G 3_prime_UTR_variant, NMD_transcript_variant 6/6

Frequencies

GnomAD3 genomes
AF:
0.108
AC:
16464
AN:
152178
Hom.:
1368
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.237
Gnomad AMI
AF:
0.0515
Gnomad AMR
AF:
0.0714
Gnomad ASJ
AF:
0.0305
Gnomad EAS
AF:
0.0202
Gnomad SAS
AF:
0.0329
Gnomad FIN
AF:
0.0851
Gnomad MID
AF:
0.0759
Gnomad NFE
AF:
0.0588
Gnomad OTH
AF:
0.0989
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.108
AC:
16519
AN:
152296
Hom.:
1380
Cov.:
33
AF XY:
0.107
AC XY:
7959
AN XY:
74484
show subpopulations
Gnomad4 AFR
AF:
0.238
Gnomad4 AMR
AF:
0.0713
Gnomad4 ASJ
AF:
0.0305
Gnomad4 EAS
AF:
0.0202
Gnomad4 SAS
AF:
0.0331
Gnomad4 FIN
AF:
0.0851
Gnomad4 NFE
AF:
0.0588
Gnomad4 OTH
AF:
0.102
Alfa
AF:
0.0926
Hom.:
119
Bravo
AF:
0.112
Asia WGS
AF:
0.0670
AC:
232
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
2.0
DANN
Benign
0.18

Splicing

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: rs6948009; hg19: chr7-116916413; API