Genetic Variant NM_182552.5:c.2524-18_2524-4delTTTTTTTTTTTTTTT (chr6-169572543-CAAAAAAAAAAAAAAA-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The NM_182552.5(WDR27):c.2524-18_2524-4delTTTTTTTTTTTTTTT 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 0.000043 ( 0 hom., cov: 0)

Consequence

WDR27
NM_182552.5 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.808

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]

WDR27 links:

ENSG00000285733 (HGNC:):

ENSG00000285733 links:

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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
WDR27	NM_182552.5 link	c.2524-18_2524-4delTTTTTTTTTTTTTTT		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
WDR27	ENST00000448612.6 link	c.2524-18_2524-4delTTTTTTTTTTTTTTT		splice_region_variant, intron_variant	Intron 24 of 25	1	NM_182552.5	ENSP00000416289.1		A2RRH5-4
ENSG00000285733	ENST00000648086.1 link	c.533+10278_533+10292delTTTTTTTTTTTTTTT		intron_variant	Intron 5 of 7			ENSP00000497979.1		A0A3B3ITY5

Frequencies

GnomAD3 genomes

AF:

0.0000433

AC:

AN:

92414

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000231

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

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

GnomAD4 genome

AF:

0.0000433

AC:

AN:

92414

Hom.:

Cov.:

AF XY:

0.0000701

AC XY:

AN XY:

42782

show subpopulations

Gnomad4 AFR

AF:

0.000231

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over