X-118392838-A-G

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7

The NM_019045.5(WDR44):ā€‹c.393A>Gā€‹(p.Glu131Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000273 in 1,098,191 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā˜…).

Frequency

Genomes: not found (cov: 24)
Exomes š‘“: 0.0000027 ( 0 hom. 1 hem. )

Consequence

WDR44
NM_019045.5 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.519
Variant links:
Genes affected
WDR44 (HGNC:30512): (WD repeat domain 44) This gene encodes a protein that interacts with the small GTPase rab11. A similar protein in rat binds the GTP-containing active form of rab11. This protein may play a role in endosome recycling. Alternate splicing results in multiple transcript variants.[provided by RefSeq, May 2010]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
Variant X-118392838-A-G is Benign according to our data. Variant chrX-118392838-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2661261.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.519 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
WDR44NM_019045.5 linkuse as main transcriptc.393A>G p.Glu131Glu synonymous_variant 4/20 ENST00000254029.8 NP_061918.3 Q5JSH3-1
WDR44NM_001184965.2 linkuse as main transcriptc.393A>G p.Glu131Glu synonymous_variant 4/20 NP_001171894.1 Q5JSH3-2
WDR44NM_001184966.1 linkuse as main transcriptc.318A>G p.Glu106Glu synonymous_variant 3/18 NP_001171895.1 Q5JSH3-4
WDR44XM_011531353.4 linkuse as main transcriptc.318A>G p.Glu106Glu synonymous_variant 3/19 XP_011529655.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
WDR44ENST00000254029.8 linkuse as main transcriptc.393A>G p.Glu131Glu synonymous_variant 4/201 NM_019045.5 ENSP00000254029.3 Q5JSH3-1

Frequencies

GnomAD3 genomes
Cov.:
24
GnomAD4 exome
AF:
0.00000273
AC:
3
AN:
1098191
Hom.:
0
Cov.:
31
AF XY:
0.00000275
AC XY:
1
AN XY:
363545
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000356
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
24

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenNov 01, 2022WDR44: PM2:Supporting, BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.57
CADD
Benign
6.0
DANN
Benign
0.33

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

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-117526801; API