3-13823578-A-G

Position:

• chr3-13823578-A-G

Variant summary

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

The NM_004625.4(WNT7A):​c.571-4155T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.705 in 152,190 control chromosomes in the GnomAD database, including 38,969 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 0.71 (38969 hom., cov: 32)
• Consequence: WNT7A NM_004625.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WNT7A	NM_004625.4	c.571-4155T>C		intron_variant		ENST00000285018.5	NP_004616.2
WNT7A	XM_011534091.3	c.370-4155T>C		intron_variant			XP_011532393.1
WNT7A	XM_047448863.1	c.370-4155T>C		intron_variant			XP_047304819.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WNT7A	ENST00000285018.5	c.571-4155T>C		intron_variant		1	NM_004625.4	ENSP00000285018	P1

Frequencies

GnomAD3 genomes AF: 0.705 AC: 107255 AN: 152072 Hom.: 38925 Cov.: 32

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.701

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.705 AC: 107359 AN: 152190 Hom.: 38969 Cov.: 32 AF XY: 0.706 AC XY: 52519 AN XY: 74388

Gnomad4 AFR AF: 0.877

Gnomad4 AMR AF: 0.642

Gnomad4 ASJ AF: 0.635

Gnomad4 EAS AF: 0.890

Gnomad4 SAS AF: 0.757

Gnomad4 FIN AF: 0.629

Gnomad4 NFE AF: 0.614

Gnomad4 OTH AF: 0.660

Alfa AF: 0.631 Hom.: 29434

Bravo AF: 0.714

Asia WGS AF: 0.816 AC: 2840 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	1.1
DANN	Benign	0.66

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: rs9840696; hg19: chr3-13865075;