11-76205463-T-C

Position:

• chr11-76205463-T-C

Variant summary

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

The NM_004626.3(WNT11):​c.83+862A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 152,138 control chromosomes in the GnomAD database, including 31,107 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 (31107 hom., cov: 33)
• Consequence: WNT11 NM_004626.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WNT11	NM_004626.3	c.83+862A>G		intron_variant		ENST00000322563.8	NP_004617.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WNT11	ENST00000322563.8	c.83+862A>G		intron_variant		1	NM_004626.3	ENSP00000325526	P1

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96796 AN: 152018 Hom.: 31069 Cov.: 33

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.650

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.637 AC: 96895 AN: 152138 Hom.: 31107 Cov.: 33 AF XY: 0.639 AC XY: 47504 AN XY: 74378

Gnomad4 AFR AF: 0.583

Gnomad4 AMR AF: 0.626

Gnomad4 ASJ AF: 0.708

Gnomad4 EAS AF: 0.808

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.643

Gnomad4 NFE AF: 0.645

Gnomad4 OTH AF: 0.657

Alfa AF: 0.629 Hom.: 3545

Bravo AF: 0.636

Asia WGS AF: 0.776 AC: 2698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.4
DANN	Benign	0.30

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: rs596339; hg19: chr11-75916507;