11-76205463-T-C

Variant names:

• chr11-76205463-T-C
• rs596339
• NM_004626.3:c.83+862A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004626.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WNT11	NM_004626.3	MANE Select	c.83+862A>G		intron	N/A	NP_004617.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WNT11	ENST00000322563.8	TSL:1 MANE Select	c.83+862A>G		intron	N/A	ENSP00000325526.3
	WNT11	ENST00000961018.1		c.83+862A>G		intron	N/A	ENSP00000631077.1
	WNT11	ENST00000961028.1		c.83+862A>G		intron	N/A	ENSP00000631087.1

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

African (AFR) AF: 0.583 AC: 24202 AN: 41496

American (AMR) AF: 0.626 AC: 9574 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2456 AN: 3470

East Asian (EAS) AF: 0.808 AC: 4169 AN: 5162

South Asian (SAS) AF: 0.730 AC: 3518 AN: 4820

European-Finnish (FIN) AF: 0.643 AC: 6818 AN: 10600

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.645 AC: 43839 AN: 67984

Other (OTH) AF: 0.657 AC: 1387 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.4
DANN	Benign	0.30
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs596339; hg19: chr11-75916507;