chr11-102801822-C-T

Variant names:

• chr11-102801822-C-T
• rs2408490
• ENST00000371455.7:n.423+3700C>T

Variant summary

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

The ENST00000525739.6(WTAPP1):​n.682+3700C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 152,032 control chromosomes in the GnomAD database, including 3,379 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 0.20 (3379 hom., cov: 32)
• Consequence: WTAPP1 ENST00000525739.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.94
• Publications: 8 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 = 0.285 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.682+3700C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WTAPP1	ENST00000371455.7	TSL:4	n.423+3700C>T		intron	N/A
	WTAPP1	ENST00000525739.6	TSL:2	n.682+3700C>T		intron	N/A
	WTAPP1	ENST00000544704.1	TSL:4	n.443+3700C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30891 AN: 151914 Hom.: 3360 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.204 AC: 30961 AN: 152032 Hom.: 3379 Cov.: 32 AF XY: 0.201 AC XY: 14958 AN XY: 74298

African (AFR) AF: 0.289 AC: 11988 AN: 41432

American (AMR) AF: 0.140 AC: 2142 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 871 AN: 3470

East Asian (EAS) AF: 0.217 AC: 1123 AN: 5172

South Asian (SAS) AF: 0.228 AC: 1098 AN: 4822

European-Finnish (FIN) AF: 0.159 AC: 1676 AN: 10558

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11395 AN: 67996

Other (OTH) AF: 0.191 AC: 404 AN: 2116

Alfa AF: 0.182 Hom.: 6214

Bravo AF: 0.204

Asia WGS AF: 0.243 AC: 844 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	0.083
DANN	Benign	0.24
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs2408490; hg19: chr11-102672553;