Menu
GeneBe

5-37479867-A-C

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_018034.4(WDR70):c.720A>C(p.Thr240=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00298 in 1,614,112 control chromosomes in the GnomAD database, including 106 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.015 ( 52 hom., cov: 32)
Exomes 𝑓: 0.0017 ( 54 hom. )

Consequence

WDR70
NM_018034.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.26
Variant links:
Genes affected
WDR70 (HGNC:25495): (WD repeat domain 70) Enables enzyme binding activity. Predicted to be involved in regulation of DNA double-strand break processing and regulation of histone H2B conserved C-terminal lysine ubiquitination. Predicted to be active in nucleus and site of double-strand break. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 5-37479867-A-C is Benign according to our data. Variant chr5-37479867-A-C is described in ClinVar as [Benign]. Clinvar id is 787284.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-1.26 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0513 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
WDR70NM_018034.4 linkuse as main transcriptc.720A>C p.Thr240= synonymous_variant 8/18 ENST00000265107.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
WDR70ENST00000265107.9 linkuse as main transcriptc.720A>C p.Thr240= synonymous_variant 8/181 NM_018034.4 P1
WDR70ENST00000504564.1 linkuse as main transcriptc.720A>C p.Thr240= synonymous_variant 8/121
WDR70ENST00000510699.1 linkuse as main transcriptn.77A>C non_coding_transcript_exon_variant 2/75
WDR70ENST00000511906.5 linkuse as main transcriptn.734A>C non_coding_transcript_exon_variant 7/152

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0152
AC:
2316
AN:
152182
Hom.:
52
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0529
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00550
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000235
Gnomad OTH
AF:
0.0105
GnomAD3 exomes
AF:
0.00411
AC:
1034
AN:
251426
Hom.:
22
AF XY:
0.00308
AC XY:
419
AN XY:
135890
show subpopulations
Gnomad AFR exome
AF:
0.0563
Gnomad AMR exome
AF:
0.00205
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000163
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000255
Gnomad OTH exome
AF:
0.00212
GnomAD4 exome
AF:
0.00170
AC:
2478
AN:
1461812
Hom.:
54
Cov.:
31
AF XY:
0.00144
AC XY:
1050
AN XY:
727210
show subpopulations
Gnomad4 AFR exome
AF:
0.0575
Gnomad4 AMR exome
AF:
0.00257
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.000209
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000146
Gnomad4 OTH exome
AF:
0.00402
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0153
AC:
2332
AN:
152300
Hom.:
52
Cov.:
32
AF XY:
0.0151
AC XY:
1125
AN XY:
74488
show subpopulations
Gnomad4 AFR
AF:
0.0531
Gnomad4 AMR
AF:
0.00549
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000235
Gnomad4 OTH
AF:
0.0104
Alfa
AF:
0.00697
Hom.:
16
Bravo
AF:
0.0176
Asia WGS
AF:
0.00404
AC:
14
AN:
3478
EpiCase
AF:
0.000273
EpiControl
AF:
0.000237

ClinVar

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

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeMay 15, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.57
Cadd
Benign
2.8
Dann
Benign
0.67
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs61742643; hg19: chr5-37479969; API