chr11-102828028-T-A

Variant names:

• chr11-102828028-T-A
• rs502588
• ENST00000371455.7:n.424-2704T>A

Variant summary

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

The ENST00000525739.6(WTAPP1):​n.683-2704T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,146 control chromosomes in the GnomAD database, including 4,540 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 0.23 (4540 hom., cov: 32)
• Consequence: WTAPP1 ENST00000525739.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.516
• Publications: 6 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=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.39 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.683-2704T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WTAPP1	ENST00000371455.7	TSL:4	n.424-2704T>A		intron	N/A
	WTAPP1	ENST00000525739.6	TSL:2	n.683-2704T>A		intron	N/A
	WTAPP1	ENST00000544704.1	TSL:4	n.444-2704T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35415 AN: 152026 Hom.: 4532 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.233 AC: 35434 AN: 152146 Hom.: 4540 Cov.: 32 AF XY: 0.239 AC XY: 17750 AN XY: 74394

African (AFR) AF: 0.197 AC: 8170 AN: 41512

American (AMR) AF: 0.374 AC: 5711 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 793 AN: 3468

East Asian (EAS) AF: 0.376 AC: 1949 AN: 5186

South Asian (SAS) AF: 0.405 AC: 1952 AN: 4822

European-Finnish (FIN) AF: 0.195 AC: 2067 AN: 10596

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 14033 AN: 67974

Other (OTH) AF: 0.233 AC: 491 AN: 2108

Alfa AF: 0.0985 Hom.: 131

Bravo AF: 0.246

Asia WGS AF: 0.342 AC: 1186 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	12
DANN	Benign	0.84
PhyloP100		0.52

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs502588;

hg19: chr11-102698759;