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GeneBe

5-37701062-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2

The NM_018034.4(WDR70):c.1197C>T(p.Asp399=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00204 in 1,605,966 control chromosomes in the GnomAD database, including 74 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.011 ( 47 hom., cov: 32)
Exomes 𝑓: 0.0011 ( 27 hom. )

Consequence

WDR70
NM_018034.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.58
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 -13 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=-0.32).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 5-37701062-C-T is Benign according to our data. Variant chr5-37701062-C-T is described in ClinVar as [Benign]. Clinvar id is 785120.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=1.58 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0111 (1689/152180) while in subpopulation AFR AF= 0.0386 (1602/41514). AF 95% confidence interval is 0.037. There are 47 homozygotes in gnomad4. There are 788 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 47 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
WDR70NM_018034.4 linkuse as main transcriptc.1197C>T p.Asp399= synonymous_variant 12/18 ENST00000265107.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
WDR70ENST00000265107.9 linkuse as main transcriptc.1197C>T p.Asp399= synonymous_variant 12/181 NM_018034.4 P1
WDR70ENST00000510699.1 linkuse as main transcriptn.554C>T non_coding_transcript_exon_variant 6/75
WDR70ENST00000511906.5 linkuse as main transcriptn.1211C>T non_coding_transcript_exon_variant 11/152

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0111
AC:
1688
AN:
152064
Hom.:
47
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0387
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00380
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000162
Gnomad OTH
AF:
0.00766
GnomAD3 exomes
AF:
0.00275
AC:
691
AN:
251124
Hom.:
11
AF XY:
0.00206
AC XY:
280
AN XY:
135758
show subpopulations
Gnomad AFR exome
AF:
0.0364
Gnomad AMR exome
AF:
0.00214
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000654
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000150
Gnomad OTH exome
AF:
0.00131
GnomAD4 exome
AF:
0.00109
AC:
1591
AN:
1453786
Hom.:
27
Cov.:
29
AF XY:
0.000968
AC XY:
701
AN XY:
723914
show subpopulations
Gnomad4 AFR exome
AF:
0.0359
Gnomad4 AMR exome
AF:
0.00242
Gnomad4 ASJ exome
AF:
0.0000383
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000929
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000100
Gnomad4 OTH exome
AF:
0.00268
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0111
AC:
1689
AN:
152180
Hom.:
47
Cov.:
32
AF XY:
0.0106
AC XY:
788
AN XY:
74396
show subpopulations
Gnomad4 AFR
AF:
0.0386
Gnomad4 AMR
AF:
0.00379
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000162
Gnomad4 OTH
AF:
0.00758
Alfa
AF:
0.00462
Hom.:
11
Bravo
AF:
0.0126
Asia WGS
AF:
0.00144
AC:
5
AN:
3478
EpiCase
AF:
0.000164
EpiControl
AF:
0.000356

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
-0.32
Cadd
Benign
13
Dann
Benign
0.83
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: rs61741266; hg19: chr5-37701164; API