chr2-63121400-TTG-T

Position:

• chr2-63121400-TTG-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_015910.7(WDPCP):​c.*604_*605del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.012 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: WDPCP NM_015910.7 3_prime_UTR
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.147

Genes affected

WDPCP (HGNC:28027): (WD repeat containing planar cell polarity effector) This gene encodes a cytoplasmic WD40 repeat protein. A similar gene in frogs encodes a planar cell polarity protein that plays a critical role in collective cell movement and ciliogenesis by mediating septin localization. Mutations in this gene are associated with Bardet-Biedl syndrome 15 and may also play a role in Meckel-Gruber syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]

(HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDPCP	NM_015910.7	c.*604_*605del		3_prime_UTR_variant	18/18	ENST00000272321.12	NP_056994.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDPCP	ENST00000272321.12	c.*604_*605del		3_prime_UTR_variant	18/18	1	NM_015910.7	ENSP00000272321	P1
	ENST00000657946.1	n.130+14393_130+14394del		intron_variant, non_coding_transcript_variant
WDPCP	ENST00000409199.5			3_prime_UTR_variant	12/12	2		ENSP00000386592
WDPCP	ENST00000409354.6	c.*894_*895del		3_prime_UTR_variant, NMD_transcript_variant	9/9	2		ENSP00000386795

Frequencies

GnomAD3 genomes AF: 0.00 AC: 988 AN: 82292 Hom.: 0 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.0116

Gnomad AMI AF: 0.0205

Gnomad AMR AF: 0.0112

Gnomad ASJ AF: 0.00967

Gnomad EAS AF: 0.0144

Gnomad SAS AF: 0.0173

Gnomad FIN AF: 0.00399

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0129

Gnomad OTH AF: 0.0131

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 88 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 72

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0120 AC: 988 AN: 82328 Hom.: 0 Cov.: 0 AF XY: 0.0109 AC XY: 435 AN XY: 39812

Gnomad4 AFR AF: 0.0115

Gnomad4 AMR AF: 0.0112

Gnomad4 ASJ AF: 0.00967

Gnomad4 EAS AF: 0.0145

Gnomad4 SAS AF: 0.0173

Gnomad4 FIN AF: 0.00399

Gnomad4 NFE AF: 0.0129

Gnomad4 OTH AF: 0.0129

Alfa AF: 0.0709 Hom.: 0

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Bardet-Biedl syndrome Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

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: rs886056219; hg19: chr2-63348535;