rs797046108

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2

The NM_001083961.2(WDR62):​c.269+12delA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00782 in 1,610,434 control chromosomes in the GnomAD database, including 140 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.0056 ( 10 hom., cov: 32)
Exomes 𝑓: 0.0081 ( 130 hom. )

Consequence

WDR62
NM_001083961.2 intron

Scores

Not classified

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:3

Conservation

PhyloP100: -0.0610
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP6
Variant 19-36058881-TA-T is Benign according to our data. Variant chr19-36058881-TA-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 212602.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Benign=3}. Variant chr19-36058881-TA-T is described in Lovd as [Likely_benign].
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0056 (854/152380) while in subpopulation SAS AF= 0.0418 (202/4834). AF 95% confidence interval is 0.0371. There are 10 homozygotes in gnomad4. There are 464 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 10 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
WDR62NM_001083961.2 linkc.269+12delA intron_variant Intron 2 of 31 ENST00000401500.7 NP_001077430.1 O43379-4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
WDR62ENST00000401500.7 linkc.269+11delA intron_variant Intron 2 of 31 1 NM_001083961.2 ENSP00000384792.1 O43379-4

Frequencies

GnomAD3 genomes
AF:
0.00561
AC:
854
AN:
152262
Hom.:
10
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000675
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00308
Gnomad ASJ
AF:
0.0268
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.0413
Gnomad FIN
AF:
0.00160
Gnomad MID
AF:
0.0222
Gnomad NFE
AF:
0.00647
Gnomad OTH
AF:
0.0105
GnomAD3 exomes
AF:
0.00963
AC:
2409
AN:
250244
Hom.:
30
AF XY:
0.0116
AC XY:
1568
AN XY:
135402
show subpopulations
Gnomad AFR exome
AF:
0.000310
Gnomad AMR exome
AF:
0.00310
Gnomad ASJ exome
AF:
0.0234
Gnomad EAS exome
AF:
0.0000545
Gnomad SAS exome
AF:
0.0380
Gnomad FIN exome
AF:
0.00194
Gnomad NFE exome
AF:
0.00692
Gnomad OTH exome
AF:
0.0125
GnomAD4 exome
AF:
0.00805
AC:
11742
AN:
1458054
Hom.:
130
Cov.:
30
AF XY:
0.00920
AC XY:
6671
AN XY:
725488
show subpopulations
Gnomad4 AFR exome
AF:
0.00117
Gnomad4 AMR exome
AF:
0.00327
Gnomad4 ASJ exome
AF:
0.0247
Gnomad4 EAS exome
AF:
0.000151
Gnomad4 SAS exome
AF:
0.0400
Gnomad4 FIN exome
AF:
0.00238
Gnomad4 NFE exome
AF:
0.00600
Gnomad4 OTH exome
AF:
0.00937
GnomAD4 genome
AF:
0.00560
AC:
854
AN:
152380
Hom.:
10
Cov.:
32
AF XY:
0.00623
AC XY:
464
AN XY:
74518
show subpopulations
Gnomad4 AFR
AF:
0.000673
Gnomad4 AMR
AF:
0.00307
Gnomad4 ASJ
AF:
0.0268
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.0418
Gnomad4 FIN
AF:
0.00160
Gnomad4 NFE
AF:
0.00647
Gnomad4 OTH
AF:
0.00992
Alfa
AF:
0.00805
Hom.:
1
Bravo
AF:
0.00472
Asia WGS
AF:
0.0110
AC:
39
AN:
3478

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:3
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 27, 2025- -
Benign, criteria provided, single submitterclinical testingGeneDxMar 03, 2015- -
Primary Microcephaly 2 With or Without Cortical Malformations Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -
not specified Benign:1
Benign, criteria provided, single submitterclinical testingGenetic Services Laboratory, University of ChicagoNov 19, 2015- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs797046108; hg19: chr19-36549783; API