rs4754880

Positions:

• chr11-102784756-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_038390.1(WTAPP1):​n.389+692G>A 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 0.19 in 152,010 control chromosomes in the GnomAD database, including 3,119 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 0.19 (3119 hom., cov: 32)
• Consequence: WTAPP1 NR_038390.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WTAPP1	NR_038390.1	n.389+692G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WTAPP1	ENST00000371455.7	n.325-13268G>A		intron_variant, non_coding_transcript_variant		4
WTAPP1	ENST00000525739.6	n.389+692G>A		intron_variant, non_coding_transcript_variant		2
WTAPP1	ENST00000544704.1	n.344+692G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28829 AN: 151892 Hom.: 3101 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.190 AC: 28864 AN: 152010 Hom.: 3119 Cov.: 32 AF XY: 0.193 AC XY: 14334 AN XY: 74322

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.182

Alfa AF: 0.199 Hom.: 5152

Bravo AF: 0.191

Asia WGS AF: 0.283 AC: 985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.3
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4754880; hg19: chr11-102655487;