19-36072155-C-T

Position:

• chr19-36072155-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001083961.2(WDR62):​c.1043+439C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,104 control chromosomes in the GnomAD database, including 6,429 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 0.28 (6429 hom., cov: 33)
• Consequence: WDR62 NM_001083961.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR62	NM_001083961.2	c.1043+439C>T		intron_variant		ENST00000401500.7	NP_001077430.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR62	ENST00000401500.7	c.1043+439C>T		intron_variant		1	NM_001083961.2	ENSP00000384792.1

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43269 AN: 151988 Hom.: 6431 Cov.: 33

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.285 AC: 43285 AN: 152104 Hom.: 6429 Cov.: 33 AF XY: 0.283 AC XY: 21028 AN XY: 74344

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.285

Alfa AF: 0.305 Hom.: 4071

Bravo AF: 0.275

Asia WGS AF: 0.204 AC: 708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.1
DANN	Benign	0.67

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: rs2023865; hg19: chr19-36563057;