dbSNP rs1799750: WTAPP1:n.423+1643delC (chr11-102799764-TC-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is . The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000525739.6(WTAPP1):n.682+1643delC variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.50 ( 18895 hom., cov: 0)

Consequence

WTAPP1
ENST00000525739.6 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0330

Publications

272 publications found

Variant links:

Genes affected

WTAPP1 (HGNC:):

WTAPP1 links:

WTAPP1 (HGNC:44115): (WTAP pseudogene 1)

WTAPP1 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000525739.6, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000525739.6. 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
	WTAPP1	NR_038390.1		n.682+1644delC		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
WTAPP1	ENST00000371455.7	TSL:4	n.423+1643delC	intron	N/A
WTAPP1	ENST00000525739.6	TSL:2	n.682+1643delC	intron	N/A
WTAPP1	ENST00000544704.1	TSL:4	n.443+1643delC	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.496

AC:

75293

AN:

151928

Hom.:

18872

Cov.:

show subpopulations

Gnomad AFR

AF:

0.532

Gnomad AMI

AF:

0.514

Gnomad AMR

AF:

0.401

Gnomad ASJ

AF:

0.496

Gnomad EAS

AF:

0.347

Gnomad SAS

AF:

0.421

Gnomad FIN

AF:

0.397

Gnomad MID

AF:

0.459

Gnomad NFE

AF:

0.527

Gnomad OTH

AF:

0.494

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.496

AC:

75350

AN:

152046

Hom.:

18895

Cov.:

AF XY:

0.487

AC XY:

36160

AN XY:

74302

show subpopulations

African (AFR)

AF:

0.532

AC:

22043

AN:

41456

American (AMR)

AF:

0.401

AC:

6122

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.496

AC:

1720

AN:

3468

East Asian (EAS)

AF:

0.347

AC:

1792

AN:

5164

South Asian (SAS)

AF:

0.421

AC:

2025

AN:

4814

European-Finnish (FIN)

AF:

0.397

AC:

4194

AN:

10562

Middle Eastern (MID)

AF:

0.456

AC:

134

AN:

294

European-Non Finnish (NFE)

AF:

0.527

AC:

35803

AN:

67982

Other (OTH)

AF:

0.497

AC:

1048

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1908

3816

5723

7631

9539

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

680

1360

2040

2720

3400

<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:

0.518

Hom.:

2475

Bravo

AF:

0.495

Asia WGS

AF:

0.393

AC:

1368

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.033

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over