11-102802517-A-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 21 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.448 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.682+4395A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WTAPP1	ENST00000371455.7	TSL:4	n.423+4395A>T		intron	N/A
	WTAPP1	ENST00000525739.6	TSL:2	n.682+4395A>T		intron	N/A
	WTAPP1	ENST00000544704.1	TSL:4	n.443+4395A>T		intron	N/A

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

African (AFR) AF: 0.405 AC: 16769 AN: 41414

American (AMR) AF: 0.329 AC: 5021 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1339 AN: 3472

East Asian (EAS) AF: 0.332 AC: 1719 AN: 5170

South Asian (SAS) AF: 0.288 AC: 1388 AN: 4820

European-Finnish (FIN) AF: 0.331 AC: 3496 AN: 10560

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30715 AN: 67960

Other (OTH) AF: 0.411 AC: 867 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.1
DANN	Benign	0.79
PhyloP100		-0.24

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: rs484915;

hg19: chr11-102673248;