Variant rs377552 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000648086.1(ENSG00000285733):c.614-538T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 152,068 control chromosomes in the GnomAD database, including 17,767 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 0.46 ( 17767 hom., cov: 32)

Consequence

ENSG00000285733
ENST00000648086.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.597

Variant links:

Genes affected

ENSG00000285733 (HGNC:):

ENSG00000285733 links:

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Protein
WDR27	XM_011535687.4 link	c.2524-538T>C	intron_variant	XP_011533989.1
WDR27	XM_011535688.4 link	c.2524-538T>C	intron_variant	XP_011533990.1
WDR27	XR_007059231.1 link	n.3192-538T>C	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	Protein	UniProt
ENSG00000285733	ENST00000648086.1 link	c.614-538T>C	intron_variant		ENSP00000497979.1	A0A3B3ITY5
ENSG00000272848	ENST00000607876.2 link	n.232-538T>C	intron_variant	6
ENSG00000285733	ENST00000649579.1 link	n.*1082-538T>C	intron_variant		ENSP00000497123.1	A0A3B3IS69
ENSG00000285733	ENST00000650382.1 link	n.1054-538T>C	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.461

AC:

69978

AN:

151950

Hom.:

17763

Cov.:

show subpopulations

Gnomad AFR

AF:

0.331

Gnomad AMI

AF:

0.577

Gnomad AMR

AF:

0.366

Gnomad ASJ

AF:

0.527

Gnomad EAS

AF:

0.0535

Gnomad SAS

AF:

0.299

Gnomad FIN

AF:

0.580

Gnomad MID

AF:

0.535

Gnomad NFE

AF:

0.579

Gnomad OTH

AF:

0.470

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

GnomAD4 genome

AF:

0.460

AC:

69987

AN:

152068

Hom.:

17767

Cov.:

AF XY:

0.452

AC XY:

33618

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.331

Gnomad4 AMR

AF:

0.365

Gnomad4 ASJ

AF:

0.527

Gnomad4 EAS

AF:

0.0529

Gnomad4 SAS

AF:

0.298

Gnomad4 FIN

AF:

0.580

Gnomad4 NFE

AF:

0.579

Gnomad4 OTH

AF:

0.464

Alfa

AF:

0.539

Hom.:

28782

Bravo

AF:

0.440

Asia WGS

AF:

0.188

AC:

657

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.9

DANN

Benign

0.53

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