chr7-117278031-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_003391.3(WNT2):​c.*124G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 1,121,734 control chromosomes in the GnomAD database, including 24,899 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 0.23 ( 4530 hom., cov: 33)
Exomes 𝑓: 0.20 ( 20369 hom. )

Consequence

WNT2
NM_003391.3 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.25
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 -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.24).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
WNT2NM_003391.3 linkuse as main transcriptc.*124G>A 3_prime_UTR_variant 5/5 ENST00000265441.8
WNT2NR_024047.2 linkuse as main transcriptn.1212G>A 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.*124G>A 3_prime_UTR_variant 5/51 NM_003391.3 P1
WNT2ENST00000449446.5 linkuse as main transcriptc.*810G>A 3_prime_UTR_variant, NMD_transcript_variant 5/53
WNT2ENST00000647844.1 linkuse as main transcriptc.*1122G>A 3_prime_UTR_variant, NMD_transcript_variant 6/6

Frequencies

GnomAD3 genomes
AF:
0.231
AC:
35190
AN:
152018
Hom.:
4526
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.329
Gnomad AMI
AF:
0.365
Gnomad AMR
AF:
0.157
Gnomad ASJ
AF:
0.204
Gnomad EAS
AF:
0.0156
Gnomad SAS
AF:
0.116
Gnomad FIN
AF:
0.163
Gnomad MID
AF:
0.212
Gnomad NFE
AF:
0.225
Gnomad OTH
AF:
0.203
GnomAD4 exome
AF:
0.196
AC:
190258
AN:
969598
Hom.:
20369
Cov.:
13
AF XY:
0.195
AC XY:
94567
AN XY:
485414
show subpopulations
Gnomad4 AFR exome
AF:
0.336
Gnomad4 AMR exome
AF:
0.121
Gnomad4 ASJ exome
AF:
0.206
Gnomad4 EAS exome
AF:
0.0150
Gnomad4 SAS exome
AF:
0.112
Gnomad4 FIN exome
AF:
0.176
Gnomad4 NFE exome
AF:
0.212
Gnomad4 OTH exome
AF:
0.191
GnomAD4 genome
AF:
0.232
AC:
35230
AN:
152136
Hom.:
4530
Cov.:
33
AF XY:
0.224
AC XY:
16690
AN XY:
74386
show subpopulations
Gnomad4 AFR
AF:
0.329
Gnomad4 AMR
AF:
0.157
Gnomad4 ASJ
AF:
0.204
Gnomad4 EAS
AF:
0.0163
Gnomad4 SAS
AF:
0.116
Gnomad4 FIN
AF:
0.163
Gnomad4 NFE
AF:
0.225
Gnomad4 OTH
AF:
0.200
Alfa
AF:
0.223
Hom.:
5378
Bravo
AF:
0.236
Asia WGS
AF:
0.0790
AC:
277
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.24
CADD
Benign
14
DANN
Benign
0.86

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: rs2228946; hg19: chr7-116918085; API