Variant chr7-135187023-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_014149.4(WDR91):c.2028G>A(p.Ser676Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 1,614,016 control chromosomes in the GnomAD database, including 436,979 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.69 ( 37348 hom., cov: 34)

Exomes 𝑓: 0.74 ( 399631 hom. )

Consequence

WDR91
NM_014149.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -4.43

Variant links:

Genes affected

WDR91 (HGNC:24997): (WD repeat domain 91) Enables phosphatidylinositol 3-kinase regulator activity. Involved in early endosome to late endosome transport; regulation of cellular protein catabolic process; and regulation of phosphatidylinositol 3-kinase activity. Located in cytosol; early endosome membrane; and late endosome membrane. Is extrinsic component of endosome membrane. [provided by Alliance of Genome Resources, Apr 2022]

WDR91 links:

WDR91 (HGNC:):

WDR91 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BP6

Variant 7-135187023-C-T is Benign according to our data. Variant chr7-135187023-C-T is described in ClinVar as [Benign]. Clinvar id is 1263809.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-4.43 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR91	NM_014149.4 linkuse as main transcript	c.2028G>A	p.Ser676Ser	synonymous_variant	14/15	ENST00000354475.5	NP_054868.3	A4D1P6-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR91	ENST00000354475.5 linkuse as main transcript	c.2028G>A	p.Ser676Ser	synonymous_variant	14/15	1	NM_014149.4	ENSP00000346466.4		A4D1P6-1
WDR91	ENST00000423565.5 linkuse as main transcript	c.1923G>A	p.Ser641Ser	synonymous_variant	14/15	5		ENSP00000392555.1		C9J1X0

Frequencies

GnomAD3 genomes

AF:

0.693

AC:

105431

AN:

152062

Hom.:

37325

Cov.:

show subpopulations

Gnomad AFR

AF:

0.537

Gnomad AMI

AF:

0.846

Gnomad AMR

AF:

0.811

Gnomad ASJ

AF:

0.723

Gnomad EAS

AF:

0.800

Gnomad SAS

AF:

0.788

Gnomad FIN

AF:

0.745

Gnomad MID

AF:

0.763

Gnomad NFE

AF:

0.734

Gnomad OTH

AF:

0.740

GnomAD3 exomes

AF:

0.751

AC:

188795

AN:

251472

Hom.:

71700

AF XY:

0.752

AC XY:

102164

AN XY:

135916

show subpopulations

Gnomad AFR exome

AF:

0.531

Gnomad AMR exome

AF:

0.871

Gnomad ASJ exome

AF:

0.730

Gnomad EAS exome

AF:

0.807

Gnomad SAS exome

AF:

0.784

Gnomad FIN exome

AF:

0.735

Gnomad NFE exome

AF:

0.732

Gnomad OTH exome

AF:

0.748

GnomAD4 exome

AF:

0.738

AC:

1078672

AN:

1461836

Hom.:

399631

Cov.:

AF XY:

0.739

AC XY:

537623

AN XY:

727210

show subpopulations

Gnomad4 AFR exome

AF:

0.525

Gnomad4 AMR exome

AF:

0.865

Gnomad4 ASJ exome

AF:

0.728

Gnomad4 EAS exome

AF:

0.805

Gnomad4 SAS exome

AF:

0.778

Gnomad4 FIN exome

AF:

0.738

Gnomad4 NFE exome

AF:

0.734

Gnomad4 OTH exome

AF:

0.735

GnomAD4 genome

AF:

0.693

AC:

105502

AN:

152180

Hom.:

37348

Cov.:

AF XY:

0.696

AC XY:

51805

AN XY:

74408

show subpopulations

Gnomad4 AFR

AF:

0.537

Gnomad4 AMR

AF:

0.812

Gnomad4 ASJ

AF:

0.723

Gnomad4 EAS

AF:

0.800

Gnomad4 SAS

AF:

0.787

Gnomad4 FIN

AF:

0.745

Gnomad4 NFE

AF:

0.734

Gnomad4 OTH

AF:

0.743

Alfa

AF:

0.731

Hom.:

82839

Bravo

AF:

0.694

Asia WGS

AF:

0.804

AC:

2792

AN:

3478

EpiCase

AF:

0.731

EpiControl

AF:

0.734

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 18, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

0.0070

DANN

Benign

0.90

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over