rs7924357

Positions:

• chr11-102757321-G-A
• chr11-102757321-G-T

Variant summary

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

The ENST00000371455.7(WTAPP1):​n.324+5895G>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 0.082 in 152,046 control chromosomes in the GnomAD database, including 690 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 0.082 (690 hom., cov: 32)
• Consequence: WTAPP1 ENST00000371455.7 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WTAPP1	ENST00000371455.7	n.324+5895G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0818 AC: 12434 AN: 151928 Hom.: 685 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0692

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0592

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0421

Gnomad OTH AF: 0.0803

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

GnomAD4 genome AF: 0.0820 AC: 12466 AN: 152046 Hom.: 690 Cov.: 32 AF XY: 0.0844 AC XY: 6272 AN XY: 74332

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.0692

Gnomad4 EAS AF: 0.269

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.0592

Gnomad4 NFE AF: 0.0421

Gnomad4 OTH AF: 0.0885

Alfa AF: 0.0517 Hom.: 677

Bravo AF: 0.0866

Asia WGS AF: 0.217 AC: 753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.55
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7924357; hg19: chr11-102628052;