19-36102943-C-A

Variant names:

• chr19-36102943-C-A
• rs587784555
• NM_001083961.2:c.3336-5C>A

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP6

The NM_001083961.2(WDR62):​c.3336-5C>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,816 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: WDR62 NM_001083961.2 splice_region, intron
• Scores: Splicing: ADA: 0.00004362
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1 B:1
• Conservation: PhyloP100: -0.847
• Publications: 0 publications found

Genes affected

WDR62 (HGNC:24502): (WD repeat domain 62) This gene is proposed to play a role in cerebral cortical development. Mutations in this gene have been associated with microencephaly, cortical malformations, and cognitive disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2011]

WDR62 Gene-Disease associations (from GenCC):

• microcephaly 2, primary, autosomal recessive, with or without cortical malformations

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine, Ambry Genetics, Illumina, G2P, ClinGen
• autosomal recessive primary microcephaly

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 19-36102943-C-A is Benign according to our data. Variant chr19-36102943-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 1298763. Variant chr19-36102943-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 1298763. Variant chr19-36102943-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 1298763. Variant chr19-36102943-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 1298763. Variant chr19-36102943-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 1298763. Variant chr19-36102943-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 1298763. Variant chr19-36102943-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 1298763. Variant chr19-36102943-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 1298763. Variant chr19-36102943-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 1298763. Variant chr19-36102943-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 1298763. Variant chr19-36102943-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 1298763. Variant chr19-36102943-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 1298763. Variant chr19-36102943-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 1298763.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDR62	NM_001083961.2	c.3336-5C>A		splice_region_variant, intron_variant	Intron 27 of 31	ENST00000401500.7	NP_001077430.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDR62	ENST00000401500.7	c.3336-5C>A		splice_region_variant, intron_variant	Intron 27 of 31	1	NM_001083961.2	ENSP00000384792.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1461816 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 727202

African (AFR) AF: 0.00 AC: 0 AN: 33480

American (AMR) AF: 0.00 AC: 0 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.00 AC: 0 AN: 86256

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53350

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5768

European-Non Finnish (NFE) AF: 0.00000180 AC: 2 AN: 1112010

Other (OTH) AF: 0.00 AC: 0 AN: 60392

GnomAD4 genome Cov.: 33

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:1 Benign:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Uncertain:1 Benign:1

Nov 11, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 01, 2021

CeGaT Center for Human Genetics Tuebingen

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.40
DANN	Benign	0.38
PhyloP100		-0.85

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000044
dbscSNV1_RF	Benign	0.020
SpliceAI score (max)		0.010		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: rs587784555; hg19: chr19-36593845;