chr6-169572543-CAAAAA-C

Variant summary

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

The NM_182552.5(WDR27):​c.2524-8_2524-4delTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0043 ( 2 hom., cov: 0)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

WDR27
NM_182552.5 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.347
Variant links:
Genes affected
WDR27 (HGNC:21248): (WD repeat domain 27) This gene encodes a protein with multiple WD repeats. Proteins with these repeats may form scaffolds for protein-protein interaction and play key roles in cell signalling. Alternative splicing results in multiple transcript variants, but the full-length structure of some of these variants cannot be determined. [provided by RefSeq, Nov 2015]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
WDR27NM_182552.5 linkc.2524-8_2524-4delTTTTT splice_region_variant, intron_variant Intron 24 of 25 ENST00000448612.6 NP_872358.4 A2RRH5-4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
WDR27ENST00000448612.6 linkc.2524-8_2524-4delTTTTT splice_region_variant, intron_variant Intron 24 of 25 1 NM_182552.5 ENSP00000416289.1 A2RRH5-4
ENSG00000285733ENST00000648086.1 linkc.533+10288_533+10292delTTTTT intron_variant Intron 5 of 7 ENSP00000497979.1 A0A3B3ITY5

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
400
AN:
92402
Hom.:
2
Cov.:
0
FAILED QC
Gnomad AFR
AF:
0.0109
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00299
Gnomad ASJ
AF:
0.000360
Gnomad EAS
AF:
0.00691
Gnomad SAS
AF:
0.00498
Gnomad FIN
AF:
0.00906
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00221
Gnomad OTH
AF:
0.000789
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
28
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
4
Gnomad4 NFE exome
AF:
0.00
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.00433
AC:
400
AN:
92384
Hom.:
2
Cov.:
0
AF XY:
0.00451
AC XY:
193
AN XY:
42758
show subpopulations
Gnomad4 AFR
AF:
0.0109
Gnomad4 AMR
AF:
0.00299
Gnomad4 ASJ
AF:
0.000360
Gnomad4 EAS
AF:
0.00692
Gnomad4 SAS
AF:
0.00502
Gnomad4 FIN
AF:
0.00906
Gnomad4 NFE
AF:
0.00221
Gnomad4 OTH
AF:
0.000785

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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: rs376783967; hg19: chr6-169972639; API