chr11-102800784-G-A

Variant summary

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

The ENST00000371455.7(WTAPP1):​n.423+2662G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.973 in 152,262 control chromosomes in the GnomAD database, including 72,181 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 0.97 ( 72181 hom., cov: 31)

Consequence

WTAPP1
ENST00000371455.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.100

Publications

3 publications found
Variant links:
Genes affected
WTAPP1 (HGNC:44115): (WTAP pseudogene 1)

Genome browser will be placed here

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=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.988 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
WTAPP1NR_038390.1 linkn.682+2662G>A intron_variant Intron 4 of 7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
WTAPP1ENST00000371455.7 linkn.423+2662G>A intron_variant Intron 3 of 4 4
WTAPP1ENST00000525739.6 linkn.682+2662G>A intron_variant Intron 4 of 7 2
WTAPP1ENST00000544704.1 linkn.443+2662G>A intron_variant Intron 2 of 3 4
WTAPP1ENST00000817290.1 linkn.287+2662G>A intron_variant Intron 3 of 4

Frequencies

GnomAD3 genomes
AF:
0.973
AC:
148016
AN:
152146
Hom.:
72124
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.996
Gnomad AMI
AF:
1.00
Gnomad AMR
AF:
0.900
Gnomad ASJ
AF:
0.982
Gnomad EAS
AF:
0.888
Gnomad SAS
AF:
0.966
Gnomad FIN
AF:
0.918
Gnomad MID
AF:
0.991
Gnomad NFE
AF:
0.990
Gnomad OTH
AF:
0.970
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.973
AC:
148129
AN:
152262
Hom.:
72181
Cov.:
31
AF XY:
0.967
AC XY:
71974
AN XY:
74418
show subpopulations
African (AFR)
AF:
0.996
AC:
41376
AN:
41558
American (AMR)
AF:
0.900
AC:
13750
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
0.982
AC:
3409
AN:
3472
East Asian (EAS)
AF:
0.888
AC:
4592
AN:
5174
South Asian (SAS)
AF:
0.966
AC:
4663
AN:
4826
European-Finnish (FIN)
AF:
0.918
AC:
9720
AN:
10584
Middle Eastern (MID)
AF:
0.990
AC:
291
AN:
294
European-Non Finnish (NFE)
AF:
0.990
AC:
67366
AN:
68046
Other (OTH)
AF:
0.971
AC:
2050
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.507
Heterozygous variant carriers
0
192
383
575
766
958
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
914
1828
2742
3656
4570
<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:
0.984
Hom.:
9289
Bravo
AF:
0.971
Asia WGS
AF:
0.941
AC:
3272
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
3.3
DANN
Benign
0.59
PhyloP100
-0.10

Splicing

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

Publications

Other links and lift over

dbSNP: rs509332; hg19: chr11-102671515; API