rs11128663

chr3-13871353-C-Gchr3-13871353-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004625.4(WNT7A):c.298+3594G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 151,940 control chromosomes in the GnomAD database, including 31,573 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 0.64 (31573 hom., cov: 31)
• Consequence: WNT7A NM_004625.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.480

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.917 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WNT7A	NM_004625.4	c.298+3594G>C		intron_variant		ENST00000285018.5
WNT7A	XM_011534091.3	c.97+3594G>C		intron_variant
WNT7A	XM_047448863.1	c.97+3594G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WNT7A	ENST00000285018.5	c.298+3594G>C		intron_variant		1	NM_004625.4	P1
WNT7A	ENST00000489346.1	n.167+3594G>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96784 AN: 151822 Hom.: 31528 Cov.: 31

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.939

Gnomad SAS AF: 0.848

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.630

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.638 AC: 96894 AN: 151940 Hom.: 31573 Cov.: 31 AF XY: 0.644 AC XY: 47791 AN XY: 74242

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.668

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.939

Gnomad4 SAS AF: 0.848

Gnomad4 FIN AF: 0.542

Gnomad4 NFE AF: 0.579

Gnomad4 OTH AF: 0.635

Alfa AF: 0.600 Hom.: 3459

Bravo AF: 0.649

Asia WGS AF: 0.870 AC: 3024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	4.8
Dann	Benign	0.70

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

Other links and lift over

dbSNP: rs11128663; hg19: chr3-13912850;