rs1124480

Positions:

• chr3-13816472-T-C

Variant summary

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

The NM_004625.4(WNT7A):​c.*2472A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 152,192 control chromosomes in the GnomAD database, including 14,880 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 0.44 (14857 hom., cov: 31)
  • Exomes 𝑓: 0.40 (23 hom.)
• Consequence: WNT7A NM_004625.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WNT7A	NM_004625.4	c.*2472A>G		3_prime_UTR_variant	4/4	ENST00000285018.5	NP_004616.2
WNT7A	XM_011534091.3	c.*2472A>G		3_prime_UTR_variant	5/5		XP_011532393.1
WNT7A	XM_047448863.1	c.*2472A>G		3_prime_UTR_variant	4/4		XP_047304819.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WNT7A	ENST00000285018.5	c.*2472A>G		3_prime_UTR_variant	4/4	1	NM_004625.4	ENSP00000285018.4

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66494 AN: 151814 Hom.: 14853 Cov.: 31

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.455

GnomAD4 exome AF: 0.396 AC: 103 AN: 260 Hom.: 23 Cov.: 0 AF XY: 0.402 AC XY: 53 AN XY: 132

Gnomad4 AFR exome AF: 0.250

Gnomad4 AMR exome AF: 0.250

Gnomad4 ASJ exome AF: 0.375

Gnomad4 EAS exome AF: 0.192

Gnomad4 FIN exome AF: 0.409

Gnomad4 NFE exome AF: 0.437

Gnomad4 OTH exome AF: 0.357

GnomAD4 genome AF: 0.438 AC: 66530 AN: 151932 Hom.: 14857 Cov.: 31 AF XY: 0.438 AC XY: 32512 AN XY: 74266

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.563

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.452

Alfa AF: 0.459 Hom.: 11358

Bravo AF: 0.426

Asia WGS AF: 0.417 AC: 1452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.8
DANN	Benign	0.35

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: rs1124480; hg19: chr3-13857969;