3-13863503-C-T

Position:

• chr3-13863503-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.299-8700G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 151,836 control chromosomes in the GnomAD database, including 28,326 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 0.59 (28326 hom., cov: 32)
• Consequence: WNT7A NM_004625.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.453

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=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WNT7A	NM_004625.4	c.299-8700G>A		intron_variant		ENST00000285018.5
WNT7A	XM_011534091.3	c.98-8700G>A		intron_variant
WNT7A	XM_047448863.1	c.98-8700G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WNT7A	ENST00000285018.5	c.299-8700G>A		intron_variant		1	NM_004625.4	P1

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89283 AN: 151718 Hom.: 28276 Cov.: 32

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.589 AC: 89402 AN: 151836 Hom.: 28326 Cov.: 32 AF XY: 0.589 AC XY: 43684 AN XY: 74162

Gnomad4 AFR AF: 0.819

Gnomad4 AMR AF: 0.524

Gnomad4 ASJ AF: 0.498

Gnomad4 EAS AF: 0.812

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.425

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.568

Alfa AF: 0.506 Hom.: 20141

Bravo AF: 0.605

Asia WGS AF: 0.695 AC: 2419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	5.4
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

Other links and lift over

dbSNP: rs9828013; hg19: chr3-13905000;