rs514921

Variant names:

• chr11-102798499-A-G
• rs514921
• ENST00000371455.7:n.423+377A>G

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000371455.7(WTAPP1):​n.423+377A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,104 control chromosomes in the GnomAD database, including 4,715 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.24 (4715 hom., cov: 32)
• Consequence: WTAPP1 ENST00000371455.7 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0260
• Publications: 28 publications found

Genes affected

WTAPP1 (HGNC:):

WTAPP1 (HGNC:44115): (WTAP pseudogene 1)

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 11-102798499-A-G is Benign according to our data. Variant chr11-102798499-A-G is described in ClinVar as Benign. ClinVar VariationId is 1266190.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WTAPP1	NR_038390.1	n.682+377A>G		intron_variant	Intron 4 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WTAPP1	ENST00000371455.7	n.423+377A>G		intron_variant	Intron 3 of 4	4
WTAPP1	ENST00000525739.6	n.682+377A>G		intron_variant	Intron 4 of 7	2
WTAPP1	ENST00000544704.1	n.443+377A>G		intron_variant	Intron 2 of 3	4
WTAPP1	ENST00000817290.1	n.287+377A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37104 AN: 151986 Hom.: 4718 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.244 AC: 37107 AN: 152104 Hom.: 4715 Cov.: 32 AF XY: 0.241 AC XY: 17947 AN XY: 74354

African (AFR) AF: 0.180 AC: 7457 AN: 41480

American (AMR) AF: 0.238 AC: 3634 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 979 AN: 3464

East Asian (EAS) AF: 0.146 AC: 753 AN: 5164

South Asian (SAS) AF: 0.300 AC: 1444 AN: 4806

European-Finnish (FIN) AF: 0.260 AC: 2757 AN: 10584

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19115 AN: 68006

Other (OTH) AF: 0.260 AC: 550 AN: 2114

Alfa AF: 0.268 Hom.: 8459

Bravo AF: 0.241

Asia WGS AF: 0.201 AC: 699 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 19, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 21964541) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.1
DANN	Benign	0.75
PhyloP100		0.026
PromoterAI		0.015	Neutral

Splicing

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

Other links and lift over

dbSNP: rs514921; hg19: chr11-102669230;