Genetic Variant WBP1L:c.*2782A>G (chr10-102816113-A-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_001083913.2(WBP1L):c.*2782A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,600 control chromosomes in the GnomAD database, including 2,217 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 0.15 ( 2195 hom., cov: 32)

Exomes 𝑓: 0.28 ( 22 hom. )

Consequence

WBP1L
NM_001083913.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.384

Publications

17 publications found

Variant links:

Genes affected

WBP1L (HGNC:23510): (WW domain binding protein 1 like) Predicted to enable ubiquitin protein ligase binding activity. Predicted to act upstream of or within CXCL12-activated CXCR4 signaling pathway; hemopoiesis; and positive regulation of protein ubiquitination. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

WBP1L links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.43).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001083913.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WBP1L	NM_001083913.2	MANE Select	c.*2782A>G		3_prime_UTR	Exon 4 of 4	NP_001077382.1
	WBP1L	NM_017787.5		c.*2782A>G		3_prime_UTR	Exon 4 of 4	NP_060257.4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
WBP1L	ENST00000448841.7	TSL:2 MANE Select	c.*2782A>G	3_prime_UTR	Exon 4 of 4	ENSP00000414721.1
WBP1L	ENST00000369889.5	TSL:1	c.*2782A>G	3_prime_UTR	Exon 4 of 4	ENSP00000358905.4
WBP1L	ENST00000647664.1		n.356-5104A>G	intron	N/A	ENSP00000498131.1

Frequencies

GnomAD3 genomes

AF:

0.150

AC:

22764

AN:

152040

Hom.:

2188

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0366

Gnomad AMI

AF:

0.120

Gnomad AMR

AF:

0.220

Gnomad ASJ

AF:

0.140

Gnomad EAS

AF:

0.149

Gnomad SAS

AF:

0.209

Gnomad FIN

AF:

0.299

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.176

Gnomad OTH

AF:

0.154

GnomAD4 exome

AF:

0.278

AC:

123

AN:

442

Hom.:

Cov.:

AF XY:

0.319

AC XY:

AN XY:

260

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.280

AC:

121

AN:

432

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AF:

0.125

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.150

AC:

22776

AN:

152158

Hom.:

2195

Cov.:

AF XY:

0.157

AC XY:

11689

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.0365

AC:

1516

AN:

41542

American (AMR)

AF:

0.221

AC:

3371

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.140

AC:

485

AN:

3466

East Asian (EAS)

AF:

0.149

AC:

774

AN:

5180

South Asian (SAS)

AF:

0.210

AC:

1012

AN:

4822

European-Finnish (FIN)

AF:

0.299

AC:

3162

AN:

10576

Middle Eastern (MID)

AF:

0.177

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.176

AC:

11972

AN:

67974

Other (OTH)

AF:

0.153

AC:

323

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

959

1917

2876

3834

4793

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

262

524

786

1048

1310

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.147

Hom.:

311

Bravo

AF:

0.140

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.43

CADD

Benign

(source)

DANN

Benign

0.71

PhyloP100

0.38

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over