chr11-76189483-T-A

Variant names:

• chr11-76189483-T-A
• rs1533763
• NM_004626.3:c.890+2081A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004626.3(WNT11):​c.890+2081A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 152,152 control chromosomes in the GnomAD database, including 3,537 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 0.20 (3537 hom., cov: 33)
• Consequence: WNT11 NM_004626.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.598
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WNT11	NM_004626.3	c.890+2081A>T		intron_variant	Intron 4 of 4	ENST00000322563.8	NP_004617.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WNT11	ENST00000322563.8	c.890+2081A>T		intron_variant	Intron 4 of 4	1	NM_004626.3	ENSP00000325526.3

Frequencies

GnomAD3 genomes AF: 0.204 AC: 31059 AN: 152034 Hom.: 3533 Cov.: 33

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.00346

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.204 AC: 31090 AN: 152152 Hom.: 3537 Cov.: 33 AF XY: 0.196 AC XY: 14601 AN XY: 74390

African (AFR) AF: 0.282 AC: 11701 AN: 41478

American (AMR) AF: 0.137 AC: 2097 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 610 AN: 3470

East Asian (EAS) AF: 0.00347 AC: 18 AN: 5184

South Asian (SAS) AF: 0.112 AC: 538 AN: 4818

European-Finnish (FIN) AF: 0.146 AC: 1548 AN: 10604

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 13975 AN: 67974

Other (OTH) AF: 0.198 AC: 419 AN: 2116

Alfa AF: 0.213 Hom.: 436

Bravo AF: 0.206

Asia WGS AF: 0.0640 AC: 226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.90
DANN	Benign	0.69
PhyloP100		-0.60
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: rs1533763; hg19: chr11-75900527;