chr2-63121380-CTT-C

Position:

• chr2-63121380-CTT-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_015910.7(WDPCP):​c.*624_*625del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 16 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.64 (15190 hom., cov: 0)
  • Exomes 𝑓: 0.31 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: WDPCP NM_015910.7 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.100

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 Benign. Variant got -10 ACMG points.

• BP6: Variant 2-63121380-CTT-C is Benign according to our data. Variant chr2-63121380-CTT-C is described in ClinVar as [Benign]. Clinvar id is 369345.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDPCP	NM_015910.7	c.*624_*625del		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.*624_*625del		3_prime_UTR_variant	18/18	1	NM_015910.7	ENSP00000272321	P1
	ENST00000657946.1	n.130+14392_130+14393del		intron_variant, non_coding_transcript_variant
WDPCP	ENST00000409199.5			downstream_gene_variant		2		ENSP00000386592
WDPCP	ENST00000409354.6			downstream_gene_variant		2		ENSP00000386795

Frequencies

GnomAD3 genomes AF: 0.00 AC: 56505 AN: 88378 Hom.: 15193 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.647

GnomAD4 exome AF: 0.313 AC: 5 AN: 16 Hom.: 0 AF XY: 0.286 AC XY: 4 AN XY: 14

Gnomad4 NFE exome AF: 0.286

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.639 AC: 56493 AN: 88364 Hom.: 15190 Cov.: 0 AF XY: 0.649 AC XY: 26482 AN XY: 40828

Gnomad4 AFR AF: 0.627

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.758

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.712

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.648

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Bardet-Biedl syndrome Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs139878372; hg19: chr2-63348515;