chr11-102785587-A-G

Variant names:

• chr11-102785587-A-G
• rs11225422
• ENST00000371455.7:n.325-12437A>G

Variant summary

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

The ENST00000371455.7(WTAPP1):​n.325-12437A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0605 in 152,252 control chromosomes in the GnomAD database, including 631 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 0.061 (631 hom., cov: 33)
• Consequence: WTAPP1 ENST00000371455.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163
• Publications: 7 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WTAPP1	NR_038390.1	n.389+1523A>G		intron_variant	Intron 1 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WTAPP1	ENST00000371455.7	n.325-12437A>G		intron_variant	Intron 2 of 4	4
WTAPP1	ENST00000525739.6	n.389+1523A>G		intron_variant	Intron 1 of 7	2
WTAPP1	ENST00000544704.1	n.344+1523A>G		intron_variant	Intron 1 of 3	4
WTAPP1	ENST00000817290.1	n.189-12437A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0605 AC: 9200 AN: 152134 Hom.: 627 Cov.: 33

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0542

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.00961

Gnomad OTH AF: 0.0659

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

GnomAD4 genome AF: 0.0605 AC: 9213 AN: 152252 Hom.: 631 Cov.: 33 AF XY: 0.0632 AC XY: 4708 AN XY: 74454

African (AFR) AF: 0.113 AC: 4673 AN: 41526

American (AMR) AF: 0.111 AC: 1705 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0542 AC: 188 AN: 3470

East Asian (EAS) AF: 0.243 AC: 1257 AN: 5168

South Asian (SAS) AF: 0.100 AC: 484 AN: 4822

European-Finnish (FIN) AF: 0.00104 AC: 11 AN: 10624

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.00962 AC: 654 AN: 68016

Other (OTH) AF: 0.0747 AC: 158 AN: 2116

Alfa AF: 0.0320 Hom.: 258

Bravo AF: 0.0709

Asia WGS AF: 0.193 AC: 668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.29
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs11225422; hg19: chr11-102656318;