rs4754880

Variant names:

• chr11-102784756-G-A
• rs4754880
• ENST00000371455.7:n.325-13268G>A

Variant summary

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

The ENST00000525739.6(WTAPP1):​n.389+692G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,010 control chromosomes in the GnomAD database, including 3,119 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 0.19 (3119 hom., cov: 32)
• Consequence: WTAPP1 ENST00000525739.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194
• Publications: 5 publications found

Genes affected

WTAPP1 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000525739.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WTAPP1	NR_038390.1		n.389+692G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WTAPP1	ENST00000371455.7	TSL:4	n.325-13268G>A		intron	N/A
	WTAPP1	ENST00000525739.6	TSL:2	n.389+692G>A		intron	N/A
	WTAPP1	ENST00000544704.1	TSL:4	n.344+692G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28829 AN: 151892 Hom.: 3101 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.190 AC: 28864 AN: 152010 Hom.: 3119 Cov.: 32 AF XY: 0.193 AC XY: 14334 AN XY: 74322

African (AFR) AF: 0.123 AC: 5108 AN: 41466

American (AMR) AF: 0.236 AC: 3605 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 454 AN: 3464

East Asian (EAS) AF: 0.460 AC: 2367 AN: 5146

South Asian (SAS) AF: 0.227 AC: 1088 AN: 4802

European-Finnish (FIN) AF: 0.194 AC: 2046 AN: 10572

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13602 AN: 67984

Other (OTH) AF: 0.182 AC: 383 AN: 2110

Alfa AF: 0.198 Hom.: 11633

Bravo AF: 0.191

Asia WGS AF: 0.283 AC: 985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.3
DANN	Benign	0.83
PhyloP100		-0.19

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4754880;

hg19: chr11-102655487;