rs527832

chr11-102831153-G-Achr11-102831153-G-T

Variant summary

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

The NR_038390.1(WTAPP1):n.762-315G>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 0.0786 in 152,188 control chromosomes in the GnomAD database, including 603 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 0.079 (603 hom., cov: 33)
• Consequence: WTAPP1 NR_038390.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238

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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WTAPP1	NR_038390.1	n.762-315G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WTAPP1	ENST00000371455.7	n.503-315G>A		intron_variant, non_coding_transcript_variant		4
WTAPP1	ENST00000525739.6	n.762-315G>A		intron_variant, non_coding_transcript_variant		2
WTAPP1	ENST00000544704.1	n.522+343G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0788 AC: 11978 AN: 152070 Hom.: 602 Cov.: 33

Gnomad AFR AF: 0.0223

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0819

Gnomad ASJ AF: 0.0533

Gnomad EAS AF: 0.0548

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.0677

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.0773

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

GnomAD4 genome AF: 0.0786 AC: 11967 AN: 152188 Hom.: 603 Cov.: 33 AF XY: 0.0777 AC XY: 5783 AN XY: 74398

Gnomad4 AFR AF: 0.0223

Gnomad4 AMR AF: 0.0818

Gnomad4 ASJ AF: 0.0533

Gnomad4 EAS AF: 0.0547

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.0677

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.0764

Alfa AF: 0.0961 Hom.: 458

Bravo AF: 0.0762

Asia WGS AF: 0.113 AC: 394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.6
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs527832; hg19: chr11-102701884;