rs11292517

Variant names:

• chr11-102799764-TC-T
• rs1799750
• ENST00000371455.7:n.423+1643delC

Variant summary

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

The ENST00000371455.7(WTAPP1):​n.423+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 ENST00000371455.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330
• Publications: 268 publications found

Genes affected

WTAPP1 (HGNC:):

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

ACMG classification

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WTAPP1	NR_038390.1	n.682+1644delC		intron_variant	Intron 4 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WTAPP1	ENST00000371455.7	n.423+1643delC		intron_variant	Intron 3 of 4	4
WTAPP1	ENST00000525739.6	n.682+1643delC		intron_variant	Intron 4 of 7	2
WTAPP1	ENST00000544704.1	n.443+1643delC		intron_variant	Intron 2 of 3	4
WTAPP1	ENST00000817290.1	n.287+1643delC		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75293 AN: 151928 Hom.: 18872 Cov.: 0

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

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

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
PhyloP100		0.033

Splicing

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

Other links and lift over

dbSNP: rs1799750; hg19: chr11-102670495;