rs41287988

Variant names:

• chr10-120908919-C-A
• rs41287988
• ENST00000497136.6:n.*3154C>A

Your query was ambiguous. Multiple possible variants found:

• chr10-120908919-C-A
• chr10-120908919-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000497136.6(WDR11):​n.*3154C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000223 in 448,534 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0000022 (0 hom.)
• Consequence: WDR11 ENST00000497136.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.94
• Publications: 2 publications found

Genes affected

WDR11 (HGNC:13831): (WD repeat domain 11) This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. This gene is located in the chromosome 10q25-26 region, which is frequently deleted in gliomas and tumors of other tissues, and is disrupted by the t(10;19) translocation rearrangement in glioblastoma cells. The gene location suggests that it is a candidate gene for the tumor suppressor locus. [provided by RefSeq, Jul 2008]

WDR11 Gene-Disease associations (from GenCC):

• hypogonadotropic hypogonadism 14 with or without anosmia

  Inheritance: AD Classification: STRONG, MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, Illumina
• intellectual developmental disorder, autosomal recessive 78

  Inheritance: AR Classification: STRONG, LIMITED Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)
• hypogonadotropic hypogonadism

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• Kallmann syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

LOC105378519 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDR11	NM_018117.12	c.*206C>A		3_prime_UTR_variant	Exon 29 of 29	ENST00000263461.11	NP_060587.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDR11	ENST00000497136.6	n.*3154C>A		non_coding_transcript_exon_variant	Exon 26 of 26	1		ENSP00000474595.1
WDR11	ENST00000605543.5	n.*2400C>A		non_coding_transcript_exon_variant	Exon 22 of 22	2		ENSP00000475076.1
WDR11	ENST00000263461.11	c.*206C>A		3_prime_UTR_variant	Exon 29 of 29	1	NM_018117.12	ENSP00000263461.5
WDR11	ENST00000497136.6	n.*3154C>A		3_prime_UTR_variant	Exon 26 of 26	1		ENSP00000474595.1
WDR11	ENST00000605543.5	n.*2400C>A		3_prime_UTR_variant	Exon 22 of 22	2		ENSP00000475076.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000223 AC: 1 AN: 448534 Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0 AN XY: 237390

African (AFR) AF: 0.00 AC: 0 AN: 12432

American (AMR) AF: 0.00 AC: 0 AN: 19526

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13868

East Asian (EAS) AF: 0.00 AC: 0 AN: 29944

South Asian (SAS) AF: 0.00 AC: 0 AN: 45530

European-Finnish (FIN) AF: 0.0000343 AC: 1 AN: 29134

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1948

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 270472

Other (OTH) AF: 0.00 AC: 0 AN: 25680

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0000113

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.084
DANN	Benign	0.71
PhyloP100		-2.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs41287988; hg19: chr10-122668431;