chr11-102820751-T-C

Variant names:

• chr11-102820751-T-C
• rs11225434
• ENST00000371455.7:n.424-9981T>C

Variant summary

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

The ENST00000525739.6(WTAPP1):​n.683-9981T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 152,024 control chromosomes in the GnomAD database, including 15,914 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 0.45 (15914 hom., cov: 31)
• Consequence: WTAPP1 ENST00000525739.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.673
• Publications: 23 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 (NFE) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000525739.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WTAPP1	NR_038390.1		n.683-9981T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WTAPP1	ENST00000371455.7	TSL:4	n.424-9981T>C		intron	N/A
	WTAPP1	ENST00000525739.6	TSL:2	n.683-9981T>C		intron	N/A
	WTAPP1	ENST00000544704.1	TSL:4	n.444-9981T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68557 AN: 151906 Hom.: 15911 Cov.: 31

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.451 AC: 68585 AN: 152024 Hom.: 15914 Cov.: 31 AF XY: 0.441 AC XY: 32803 AN XY: 74302

African (AFR) AF: 0.416 AC: 17254 AN: 41438

American (AMR) AF: 0.374 AC: 5723 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1368 AN: 3472

East Asian (EAS) AF: 0.323 AC: 1666 AN: 5162

South Asian (SAS) AF: 0.303 AC: 1459 AN: 4816

European-Finnish (FIN) AF: 0.395 AC: 4172 AN: 10568

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.522 AC: 35456 AN: 67970

Other (OTH) AF: 0.462 AC: 975 AN: 2112

Alfa AF: 0.496 Hom.: 54916

Bravo AF: 0.449

Asia WGS AF: 0.340 AC: 1183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.54
DANN	Benign	0.70
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs11225434; hg19: chr11-102691482;