chr11-102800784-G-A

Variant names:

• chr11-102800784-G-A
• rs509332
• ENST00000371455.7:n.423+2662G>A

Variant summary

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

The ENST00000371455.7(WTAPP1):​n.423+2662G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.973 in 152,262 control chromosomes in the GnomAD database, including 72,181 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 0.97 (72181 hom., cov: 31)
• Consequence: WTAPP1 ENST00000371455.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.988 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WTAPP1	NR_038390.1	n.682+2662G>A		intron_variant	Intron 4 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WTAPP1	ENST00000371455.7	n.423+2662G>A		intron_variant	Intron 3 of 4	4
WTAPP1	ENST00000525739.6	n.682+2662G>A		intron_variant	Intron 4 of 7	2
WTAPP1	ENST00000544704.1	n.443+2662G>A		intron_variant	Intron 2 of 3	4
WTAPP1	ENST00000817290.1	n.287+2662G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.973 AC: 148016 AN: 152146 Hom.: 72124 Cov.: 31

Gnomad AFR AF: 0.996

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.900

Gnomad ASJ AF: 0.982

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.966

Gnomad FIN AF: 0.918

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.990

Gnomad OTH AF: 0.970

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

GnomAD4 genome AF: 0.973 AC: 148129 AN: 152262 Hom.: 72181 Cov.: 31 AF XY: 0.967 AC XY: 71974 AN XY: 74418

African (AFR) AF: 0.996 AC: 41376 AN: 41558

American (AMR) AF: 0.900 AC: 13750 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.982 AC: 3409 AN: 3472

East Asian (EAS) AF: 0.888 AC: 4592 AN: 5174

South Asian (SAS) AF: 0.966 AC: 4663 AN: 4826

European-Finnish (FIN) AF: 0.918 AC: 9720 AN: 10584

Middle Eastern (MID) AF: 0.990 AC: 291 AN: 294

European-Non Finnish (NFE) AF: 0.990 AC: 67366 AN: 68046

Other (OTH) AF: 0.971 AC: 2050 AN: 2112

Alfa AF: 0.984 Hom.: 9289

Bravo AF: 0.971

Asia WGS AF: 0.941 AC: 3272 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	3.3
DANN	Benign	0.59
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs509332; hg19: chr11-102671515;