ENST00000371455.7:n.423+11113G>C

Variant names:

• chr11-102809235-G-C
• rs12289128
• ENST00000371455.7:n.423+11113G>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000371455.7(WTAPP1):​n.423+11113G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0935 in 152,182 control chromosomes in the GnomAD database, including 755 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 0.094 (755 hom., cov: 33)
• Consequence: WTAPP1 ENST00000371455.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.752

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WTAPP1	NR_038390.1	n.682+11113G>C		intron_variant	Intron 4 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WTAPP1	ENST00000371455.7	n.423+11113G>C		intron_variant	Intron 3 of 4	4
WTAPP1	ENST00000525739.6	n.682+11113G>C		intron_variant	Intron 4 of 7	2
WTAPP1	ENST00000544704.1	n.443+11113G>C		intron_variant	Intron 2 of 3	4

Frequencies

GnomAD3 genomes AF: 0.0935 AC: 14217 AN: 152064 Hom.: 754 Cov.: 33

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.0709

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.0669

Gnomad FIN AF: 0.0574

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0846

Gnomad OTH AF: 0.0876

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

GnomAD4 genome AF: 0.0935 AC: 14232 AN: 152182 Hom.: 755 Cov.: 33 AF XY: 0.0918 AC XY: 6833 AN XY: 74398

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.0708

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.0676

Gnomad4 FIN AF: 0.0574

Gnomad4 NFE AF: 0.0846

Gnomad4 OTH AF: 0.0866

Alfa AF: 0.0377 Hom.: 30

Bravo AF: 0.0960

Asia WGS AF: 0.0400 AC: 140 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.92
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12289128; hg19: chr11-102679966;