11-102798678-T-C

Variant names:

• chr11-102798678-T-C
• rs1144393
• ENST00000371455.7:n.423+556T>C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000525739.6(WTAPP1):​n.682+556T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 151,960 control chromosomes in the GnomAD database, including 7,205 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.29 (7205 hom., cov: 31)
• Consequence: WTAPP1 ENST00000525739.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.45

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 11-102798678-T-C is Benign according to our data. Variant chr11-102798678-T-C is described in ClinVar as [Benign]. Clinvar id is 1229767.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WTAPP1	NR_038390.1	n.682+556T>C		intron_variant	Intron 4 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WTAPP1	ENST00000371455.7	n.423+556T>C		intron_variant	Intron 3 of 4	4
WTAPP1	ENST00000525739.6	n.682+556T>C		intron_variant	Intron 4 of 7	2
WTAPP1	ENST00000544704.1	n.443+556T>C		intron_variant	Intron 2 of 3	4

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44667 AN: 151842 Hom.: 7202 Cov.: 31

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.0869

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.294 AC: 44669 AN: 151960 Hom.: 7205 Cov.: 31 AF XY: 0.286 AC XY: 21214 AN XY: 74268

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.0869

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.304

Alfa AF: 0.359 Hom.: 10461

Bravo AF: 0.286

Asia WGS AF: 0.108 AC: 379 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Sep 22, 2020

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 18602909, 19406964, 16210545) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.52
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1144393; hg19: chr11-102669409;