ENST00000371455.7:n.423+357A>G

Variant names:

• chr11-102798479-A-G
• rs494379
• ENST00000371455.7:n.423+357A>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+357A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,030 control chromosomes in the GnomAD database, including 5,433 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.25 (5433 hom., cov: 32)
• Consequence: WTAPP1 ENST00000371455.7 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.10
• Publications: 50 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=-0.94).
• BP6: Variant 11-102798479-A-G is Benign according to our data. Variant chr11-102798479-A-G is described in ClinVar as Benign. ClinVar VariationId is 1236601.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000371455.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WTAPP1	NR_038390.1		n.682+357A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WTAPP1	ENST00000371455.7	TSL:4	n.423+357A>G		intron	N/A
	WTAPP1	ENST00000525739.6	TSL:2	n.682+357A>G		intron	N/A
	WTAPP1	ENST00000544704.1	TSL:4	n.443+357A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38433 AN: 151912 Hom.: 5408 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.253 AC: 38500 AN: 152030 Hom.: 5433 Cov.: 32 AF XY: 0.255 AC XY: 18974 AN XY: 74320

African (AFR) AF: 0.319 AC: 13209 AN: 41470

American (AMR) AF: 0.177 AC: 2709 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 862 AN: 3468

East Asian (EAS) AF: 0.577 AC: 2978 AN: 5162

South Asian (SAS) AF: 0.294 AC: 1416 AN: 4816

European-Finnish (FIN) AF: 0.234 AC: 2475 AN: 10558

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 13980 AN: 67972

Other (OTH) AF: 0.252 AC: 533 AN: 2114

Alfa AF: 0.222 Hom.: 5716

Bravo AF: 0.252

Asia WGS AF: 0.469 AC: 1630 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 12, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.083
DANN	Benign	0.36
PhyloP100		-1.1
PromoterAI		-0.0034	Neutral

Splicing

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

Other links and lift over

dbSNP: rs494379; hg19: chr11-102669210;