11-76203043-A-G

Variant names:

• chr11-76203043-A-G
• rs689095
• NM_004626.3:c.83+3282T>C

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+3282T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 152,070 control chromosomes in the GnomAD database, including 8,922 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 0.34 (8922 hom., cov: 33)
• Consequence: WNT11 NM_004626.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.756
• Publications: 13 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.535 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+3282T>C		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+3282T>C		intron	N/A	ENSP00000325526.3

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51513 AN: 151952 Hom.: 8908 Cov.: 33

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.339 AC: 51582 AN: 152070 Hom.: 8922 Cov.: 33 AF XY: 0.344 AC XY: 25563 AN XY: 74338

African (AFR) AF: 0.300 AC: 12470 AN: 41498

American (AMR) AF: 0.373 AC: 5704 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1256 AN: 3464

East Asian (EAS) AF: 0.552 AC: 2848 AN: 5160

South Asian (SAS) AF: 0.436 AC: 2103 AN: 4820

European-Finnish (FIN) AF: 0.376 AC: 3971 AN: 10552

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21854 AN: 67984

Other (OTH) AF: 0.349 AC: 737 AN: 2110

Alfa AF: 0.334 Hom.: 33431

Bravo AF: 0.341

Asia WGS AF: 0.479 AC: 1664 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.73
PhyloP100		-0.76
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: rs689095; hg19: chr11-75914087;