rs1799750

chr11-102799764-TC-T

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. 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330

Genes affected

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

ACMG classification

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
WTAPP1	NR_038390.1	n.682+1644del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WTAPP1	ENST00000371455.7	n.423+1644del		intron_variant, non_coding_transcript_variant		4
WTAPP1	ENST00000525739.6	n.682+1644del		intron_variant, non_coding_transcript_variant		2
WTAPP1	ENST00000544704.1	n.443+1644del		intron_variant, non_coding_transcript_variant		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

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1799750; hg19: chr11-102670495;