rs514921

chr11-102798499-A-G

Variant summary

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

The NR_038390.1(WTAPP1):n.682+377A>G variant causes a intron, non coding transcript 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 NR_038390.1 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0260

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=-0.84).
• BP6: Variant 11-102798499-A-G is Benign according to our data. Variant chr11-102798499-A-G is described in ClinVar as [Benign]. Clinvar id 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/exons	MANE	UniProt
WTAPP1	NR_038390.1	n.682+377A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WTAPP1	ENST00000371455.7	n.423+377A>G		intron_variant, non_coding_transcript_variant		4
WTAPP1	ENST00000525739.6	n.682+377A>G		intron_variant, non_coding_transcript_variant		2
WTAPP1	ENST00000544704.1	n.443+377A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.260

Alfa AF: 0.274 Hom.: 6067

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

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs514921; hg19: chr11-102669230;