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GeneBe

rs1799750

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NR_038390.1(WTAPP1):n.682+1644del variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 152,046 control chromosomes in the GnomAD database, including 18,895 homozygotes. 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
NR_038390.1 intron, non_coding_transcript

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0330
Variant links:
Genes affected
WTAPP1 (HGNC:44115): (WTAP pseudogene 1)

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
WTAPP1NR_038390.1 linkuse as main transcriptn.682+1644del intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
WTAPP1ENST00000371455.7 linkuse as main transcriptn.423+1644del intron_variant, non_coding_transcript_variant 4
WTAPP1ENST00000525739.6 linkuse as main transcriptn.682+1644del intron_variant, non_coding_transcript_variant 2
WTAPP1ENST00000544704.1 linkuse as main transcriptn.443+1644del intron_variant, non_coding_transcript_variant 4

Frequencies

GnomAD3 genomes
AF:
0.496
AC:
75293
AN:
151928
Hom.:
18872
Cov.:
0
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.:
0
AF XY:
0.487
AC XY:
36160
AN XY:
74302
show subpopulations
Gnomad4 AFR
AF:
0.532
Gnomad4 AMR
AF:
0.401
Gnomad4 ASJ
AF:
0.496
Gnomad4 EAS
AF:
0.347
Gnomad4 SAS
AF:
0.421
Gnomad4 FIN
AF:
0.397
Gnomad4 NFE
AF:
0.527
Gnomad4 OTH
AF:
0.497
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 v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1799750; hg19: chr11-102670495; API