11-102785475-T-C

Variant names:

• chr11-102785475-T-C
• rs470226
• ENST00000371455.7:n.325-12549T>C

Variant summary

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

The ENST00000371455.7(WTAPP1):​n.325-12549T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.949 in 152,314 control chromosomes in the GnomAD database, including 68,643 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 0.95 (68643 hom., cov: 33)
• Consequence: WTAPP1 ENST00000371455.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.59
• Publications: 4 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.98 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WTAPP1	NR_038390.1	n.389+1411T>C		intron_variant	Intron 1 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WTAPP1	ENST00000371455.7	n.325-12549T>C		intron_variant	Intron 2 of 4	4
WTAPP1	ENST00000525739.6	n.389+1411T>C		intron_variant	Intron 1 of 7	2
WTAPP1	ENST00000544704.1	n.344+1411T>C		intron_variant	Intron 1 of 3	4
WTAPP1	ENST00000817290.1	n.189-12549T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.949 AC: 144383 AN: 152196 Hom.: 68585 Cov.: 33

Gnomad AFR AF: 0.988

Gnomad AMI AF: 0.932

Gnomad AMR AF: 0.902

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.917

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.949

Gnomad OTH AF: 0.939

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

GnomAD4 genome AF: 0.949 AC: 144500 AN: 152314 Hom.: 68643 Cov.: 33 AF XY: 0.945 AC XY: 70377 AN XY: 74456

African (AFR) AF: 0.988 AC: 41090 AN: 41590

American (AMR) AF: 0.903 AC: 13809 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.921 AC: 3199 AN: 3472

East Asian (EAS) AF: 0.895 AC: 4630 AN: 5176

South Asian (SAS) AF: 0.903 AC: 4357 AN: 4826

European-Finnish (FIN) AF: 0.917 AC: 9715 AN: 10596

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.949 AC: 64595 AN: 68040

Other (OTH) AF: 0.939 AC: 1982 AN: 2110

Alfa AF: 0.925 Hom.: 5922

Bravo AF: 0.948

Asia WGS AF: 0.910 AC: 3166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.32
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs470226; hg19: chr11-102656206; COSMIC: COSV54247520;