chr11-102801718-T-G

Variant names:

• chr11-102801718-T-G
• rs1155764
• ENST00000371455.7:n.423+3596T>G

Variant summary

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

The ENST00000371455.7(WTAPP1):​n.423+3596T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,126 control chromosomes in the GnomAD database, including 3,458 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 0.21 (3458 hom., cov: 32)
• Consequence: WTAPP1 ENST00000371455.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.79
• Publications: 10 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WTAPP1	NR_038390.1	n.682+3596T>G		intron_variant	Intron 4 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WTAPP1	ENST00000371455.7	n.423+3596T>G		intron_variant	Intron 3 of 4	4
WTAPP1	ENST00000525739.6	n.682+3596T>G		intron_variant	Intron 4 of 7	2
WTAPP1	ENST00000544704.1	n.443+3596T>G		intron_variant	Intron 2 of 3	4
WTAPP1	ENST00000817290.1	n.287+3596T>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31264 AN: 152008 Hom.: 3439 Cov.: 32

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.206 AC: 31338 AN: 152126 Hom.: 3458 Cov.: 32 AF XY: 0.204 AC XY: 15176 AN XY: 74364

African (AFR) AF: 0.291 AC: 12058 AN: 41470

American (AMR) AF: 0.157 AC: 2403 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 869 AN: 3466

East Asian (EAS) AF: 0.222 AC: 1150 AN: 5178

South Asian (SAS) AF: 0.228 AC: 1096 AN: 4816

European-Finnish (FIN) AF: 0.158 AC: 1678 AN: 10590

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11409 AN: 68002

Other (OTH) AF: 0.195 AC: 411 AN: 2110

Alfa AF: 0.189 Hom.: 1246

Bravo AF: 0.207

Asia WGS AF: 0.248 AC: 861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.3
DANN	Benign	0.78
PhyloP100		2.8

Splicing

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

Other links and lift over

dbSNP: rs1155764; hg19: chr11-102672449;