rs502588

chr11-102828028-T-Achr11-102828028-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_038390.1(WTAPP1):n.683-2704T>A 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 0.233 in 152,146 control chromosomes in the GnomAD database, including 4,540 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 0.23 (4540 hom., cov: 32)
• Consequence: WTAPP1 NR_038390.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.516

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WTAPP1	NR_038390.1	n.683-2704T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WTAPP1	ENST00000371455.7	n.424-2704T>A		intron_variant, non_coding_transcript_variant		4
WTAPP1	ENST00000525739.6	n.683-2704T>A		intron_variant, non_coding_transcript_variant		2
WTAPP1	ENST00000544704.1	n.444-2704T>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35415 AN: 152026 Hom.: 4532 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.233

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.233 AC: 35434 AN: 152146 Hom.: 4540 Cov.: 32 AF XY: 0.239 AC XY: 17750 AN XY: 74394

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.233

Alfa AF: 0.0985 Hom.: 131

Bravo AF: 0.246

Asia WGS AF: 0.342 AC: 1186 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	12
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs502588; hg19: chr11-102698759;