rs1568507

Positions:

• chr11-76208275-T-A
• chr11-76208275-T-C

Variant summary

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

The ENST00000529461.1(WNT11):​c.-172-1320A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 152,156 control chromosomes in the GnomAD database, including 8,544 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 0.33 (8544 hom., cov: 33)
• Consequence: WNT11 ENST00000529461.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.801

Genes affected

WNT11 (HGNC:12776): (Wnt family member 11) The WNT gene family consists of structurally related genes which 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 a member of the WNT gene family. It encodes a protein which shows 97%, 85%, and 63% amino acid identity with mouse, chicken, and Xenopus Wnt11 protein, respectively. This gene may play roles in the development of skeleton, kidney and lung, and is considered to be a plausible candidate gene for High Bone Mass Syndrome. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WNT11	XM_005274231.2	c.-91-1777A>T		intron_variant
WNT11	XM_011545238.2	c.-91-1777A>T		intron_variant
WNT11	XM_011545239.3	c.-91-1777A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WNT11	ENST00000529461.1	c.-172-1320A>T		intron_variant		2
WNT11	ENST00000532150.1	n.385-1777A>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50177 AN: 152038 Hom.: 8523 Cov.: 33

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.330 AC: 50244 AN: 152156 Hom.: 8544 Cov.: 33 AF XY: 0.335 AC XY: 24925 AN XY: 74368

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.353

Alfa AF: 0.170 Hom.: 307

Bravo AF: 0.332

Asia WGS AF: 0.484 AC: 1683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.8
DANN	Benign	0.55

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1568507; hg19: chr11-75919319;