3-13846232-C-T

Variant summary

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

The NM_004625.4(WNT7A):​c.570+8300G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 152,134 control chromosomes in the GnomAD database, including 10,560 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 0.37 ( 10560 hom., cov: 33)

Consequence

WNT7A
NM_004625.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.18
Variant links:
Genes affected
WNT7A (HGNC:12786): (Wnt family member 7A) This gene is a member of the WNT gene family, which consists of structurally related genes that 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 involved in the development of the anterior-posterior axis in the female reproductive tract, and also plays a critical role in uterine smooth muscle pattering and maintenance of adult uterine function. Mutations in this gene are associated with Fuhrmann and Al-Awadi/Raas-Rothschild/Schinzel phocomelia syndromes. [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=-0.94).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
WNT7ANM_004625.4 linkuse as main transcriptc.570+8300G>A intron_variant ENST00000285018.5 NP_004616.2 O00755
WNT7AXM_011534091.3 linkuse as main transcriptc.369+8300G>A intron_variant XP_011532393.1
WNT7AXM_047448863.1 linkuse as main transcriptc.369+8300G>A intron_variant XP_047304819.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
WNT7AENST00000285018.5 linkuse as main transcriptc.570+8300G>A intron_variant 1 NM_004625.4 ENSP00000285018.4 O00755

Frequencies

GnomAD3 genomes
AF:
0.366
AC:
55660
AN:
152016
Hom.:
10538
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.469
Gnomad AMI
AF:
0.328
Gnomad AMR
AF:
0.343
Gnomad ASJ
AF:
0.378
Gnomad EAS
AF:
0.347
Gnomad SAS
AF:
0.471
Gnomad FIN
AF:
0.283
Gnomad MID
AF:
0.421
Gnomad NFE
AF:
0.315
Gnomad OTH
AF:
0.379
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.366
AC:
55721
AN:
152134
Hom.:
10560
Cov.:
33
AF XY:
0.367
AC XY:
27305
AN XY:
74372
show subpopulations
Gnomad4 AFR
AF:
0.469
Gnomad4 AMR
AF:
0.344
Gnomad4 ASJ
AF:
0.378
Gnomad4 EAS
AF:
0.347
Gnomad4 SAS
AF:
0.470
Gnomad4 FIN
AF:
0.283
Gnomad4 NFE
AF:
0.315
Gnomad4 OTH
AF:
0.386
Alfa
AF:
0.248
Hom.:
701
Bravo
AF:
0.372
Asia WGS
AF:
0.431
AC:
1499
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.10
DANN
Benign
0.73

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: rs934450; hg19: chr3-13887729; API