rs7924357

Variant names:

• chr11-102757321-G-A
• rs7924357
• ENST00000371455.7:n.324+5895G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000371455.7(WTAPP1):​n.324+5895G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 8 publications found

Genes affected

WTAPP1 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WTAPP1	ENST00000371455.7	n.324+5895G>A		intron_variant	Intron 2 of 4	4
WTAPP1	ENST00000817290.1	n.188+5895G>A		intron_variant	Intron 2 of 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

African (AFR) AF: 0.116 AC: 4820 AN: 41444

American (AMR) AF: 0.107 AC: 1640 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0692 AC: 240 AN: 3470

East Asian (EAS) AF: 0.269 AC: 1391 AN: 5172

South Asian (SAS) AF: 0.125 AC: 604 AN: 4814

European-Finnish (FIN) AF: 0.0592 AC: 626 AN: 10580

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0421 AC: 2863 AN: 67984

Other (OTH) AF: 0.0885 AC: 187 AN: 2114

Alfa AF: 0.0573 Hom.: 1247

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7924357; hg19: chr11-102628052;