11-102802517-A-T

Variant names:

• chr11-102802517-A-T
• rs484915
• ENST00000371455.7:n.423+4395A>T

Variant summary

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

The ENST00000525739.6(WTAPP1):​n.682+4395A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 151,988 control chromosomes in the GnomAD database, including 12,718 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 0.41 (12718 hom., cov: 32)
• Consequence: WTAPP1 ENST00000525739.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WTAPP1	NR_038390.1	n.682+4395A>T		intron_variant	Intron 4 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WTAPP1	ENST00000371455.7	n.423+4395A>T		intron_variant	Intron 3 of 4	4
WTAPP1	ENST00000525739.6	n.682+4395A>T		intron_variant	Intron 4 of 7	2
WTAPP1	ENST00000544704.1	n.443+4395A>T		intron_variant	Intron 2 of 3	4

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61747 AN: 151870 Hom.: 12717 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.406 AC: 61774 AN: 151988 Hom.: 12718 Cov.: 32 AF XY: 0.398 AC XY: 29607 AN XY: 74320

Gnomad4 AFR AF: 0.405

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.411

Alfa AF: 0.437 Hom.: 2035

Bravo AF: 0.405

Asia WGS AF: 0.325 AC: 1132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.1
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs484915; hg19: chr11-102673248;