rs1799750

Variant summary

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

The NR_038390(WTAPP1):n.682+1644del variant causes a intron, non coding transcript 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 ( 18872 hom., cov: 0)

Consequence

WTAPP1
NR_038390 intron, non_coding_transcript

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0330

Links

WTAPP1 (HGNC:44115):

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd 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
WTAPP1	NR_038390.1 linkuse as main transcript	n.682+1644del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
WTAPP1	ENST00000371455.7 linkuse as main transcript	n.423+1644del	intron_variant, non_coding_transcript_variant	4
WTAPP1	ENST00000525739.6 linkuse as main transcript	n.682+1644del	intron_variant, non_coding_transcript_variant	2
WTAPP1	ENST00000544704.1 linkuse as main transcript	n.443+1644del	intron_variant, non_coding_transcript_variant	4

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

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.