Genetic Variant WBP1L:c.*1241A>T (chr10-102814572-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001083913.2(WBP1L):c.*1241A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 148,536 control chromosomes in the GnomAD database, including 24,158 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 0.57 ( 24079 hom., cov: 23)

Exomes 𝑓: 0.58 ( 79 hom. )

Consequence

WBP1L
NM_001083913.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.363

Publications

15 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.64).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.62 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WBP1L	NM_001083913.2	MANE Select	c.*1241A>T		3_prime_UTR	Exon 4 of 4	NP_001077382.1	Q9NX94-2
	WBP1L	NM_017787.5		c.*1241A>T		3_prime_UTR	Exon 4 of 4	NP_060257.4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
WBP1L	ENST00000448841.7	TSL:2 MANE Select	c.*1241A>T	3_prime_UTR	Exon 4 of 4	ENSP00000414721.1	Q9NX94-2
WBP1L	ENST00000369889.5	TSL:1	c.*1241A>T	3_prime_UTR	Exon 4 of 4	ENSP00000358905.4	Q9NX94-1
WBP1L	ENST00000863249.1		c.*1241A>T	3_prime_UTR	Exon 3 of 3	ENSP00000533308.1

Frequencies

GnomAD3 genomes

AF:

0.569

AC:

84278

AN:

147998

Hom.:

24060

Cov.:

show subpopulations

Gnomad AFR

AF:

0.528

Gnomad AMI

AF:

0.698

Gnomad AMR

AF:

0.593

Gnomad ASJ

AF:

0.629

Gnomad EAS

AF:

0.423

Gnomad SAS

AF:

0.641

Gnomad FIN

AF:

0.631

Gnomad MID

AF:

0.649

Gnomad NFE

AF:

0.580

Gnomad OTH

AF:

0.587

GnomAD4 exome

AF:

0.584

AC:

250

AN:

428

Hom.:

Cov.:

AF XY:

0.605

AC XY:

155

AN XY:

256

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:

0.585

AC:

242

AN:

414

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.625

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.472

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:

0.569

AC:

84342

AN:

148108

Hom.:

24079

Cov.:

AF XY:

0.573

AC XY:

41197

AN XY:

71884

show subpopulations

African (AFR)

AF:

0.529

AC:

21096

AN:

39894

American (AMR)

AF:

0.594

AC:

8842

AN:

14896

Ashkenazi Jewish (ASJ)

AF:

0.629

AC:

2176

AN:

3458

East Asian (EAS)

AF:

0.424

AC:

2114

AN:

4988

South Asian (SAS)

AF:

0.639

AC:

3004

AN:

4698

European-Finnish (FIN)

AF:

0.631

AC:

6056

AN:

9600

Middle Eastern (MID)

AF:

0.643

AC:

189

AN:

294

European-Non Finnish (NFE)

AF:

0.580

AC:

39037

AN:

67328

Other (OTH)

AF:

0.585

AC:

1196

AN:

2046

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.516

Heterozygous variant carriers

1722

3444

5165

6887

8609

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

730

1460

2190

2920

3650

<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:

0.561

Hom.:

3004

Bravo

AF:

0.563

Asia WGS

AF:

0.572

AC:

1991

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

9.1

(source)

DANN

Benign

0.83

PhyloP100

-0.36

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