Genetic Variant NM_001083913.2: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:

Genome browser will be placed here

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
WBP1L	NM_001083913.2 link	c.*2782A>G	3_prime_UTR_variant	Exon 4 of 4	ENST00000448841.7	NP_001077382.1	Q9NX94-2
WBP1L	NM_017787.5 link	c.*2782A>G	3_prime_UTR_variant	Exon 4 of 4		NP_060257.4	Q9NX94-1
WBP1L	XM_011539913.3 link	c.*2782A>G	3_prime_UTR_variant	Exon 4 of 4		XP_011538215.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
WBP1L	ENST00000448841.7 link	c.*2782A>G	3_prime_UTR_variant	Exon 4 of 4	2	NM_001083913.2	ENSP00000414721.1	Q9NX94-2
WBP1L	ENST00000369889.5 link	c.*2782A>G	3_prime_UTR_variant	Exon 4 of 4	1		ENSP00000358905.4	Q9NX94-1
WBP1L	ENST00000647664.1 link	n.356-5104A>G	intron_variant	Intron 3 of 7			ENSP00000498131.1	A0A3B3IU90

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over