rs2155013

Variant names:

• chr11-102831127-T-C
• rs2155013
• ENST00000371455.7:n.502+317T>C

Variant summary

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

The ENST00000371455.7(WTAPP1):​n.502+317T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 151,972 control chromosomes in the GnomAD database, including 15,569 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 (15569 hom., cov: 31)
• Consequence: WTAPP1 ENST00000371455.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.411
• 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WTAPP1	NR_038390.1	n.761+317T>C		intron_variant	Intron 5 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WTAPP1	ENST00000371455.7	n.502+317T>C		intron_variant	Intron 4 of 4	4
WTAPP1	ENST00000525739.6	n.761+317T>C		intron_variant	Intron 5 of 7	2
WTAPP1	ENST00000544704.1	n.522+317T>C		intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67889 AN: 151854 Hom.: 15566 Cov.: 31

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.447 AC: 67917 AN: 151972 Hom.: 15569 Cov.: 31 AF XY: 0.438 AC XY: 32530 AN XY: 74298

African (AFR) AF: 0.423 AC: 17544 AN: 41458

American (AMR) AF: 0.370 AC: 5653 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1327 AN: 3462

East Asian (EAS) AF: 0.322 AC: 1666 AN: 5168

South Asian (SAS) AF: 0.303 AC: 1456 AN: 4812

European-Finnish (FIN) AF: 0.392 AC: 4140 AN: 10556

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.510 AC: 34667 AN: 67924

Other (OTH) AF: 0.456 AC: 959 AN: 2104

Alfa AF: 0.462 Hom.: 2666

Bravo AF: 0.445

Asia WGS AF: 0.336 AC: 1170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.7
DANN	Benign	0.68
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs2155013; hg19: chr11-102701858;