rs502174

chr11-102811772-A-Cchr11-102811772-A-G

Variant summary

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

The NR_038390.1(WTAPP1):n.682+13650A>C 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 0.444 in 151,768 control chromosomes in the GnomAD database, including 15,313 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 0.44 (15313 hom., cov: 30)
• Consequence: WTAPP1 NR_038390.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WTAPP1	NR_038390.1	n.682+13650A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WTAPP1	ENST00000371455.7	n.423+13650A>C		intron_variant, non_coding_transcript_variant		4
WTAPP1	ENST00000525739.6	n.682+13650A>C		intron_variant, non_coding_transcript_variant		2
WTAPP1	ENST00000544704.1	n.443+13650A>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67411 AN: 151650 Hom.: 15307 Cov.: 30

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.444 AC: 67442 AN: 151768 Hom.: 15313 Cov.: 30 AF XY: 0.435 AC XY: 32276 AN XY: 74168

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.323

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.464

Alfa AF: 0.436 Hom.: 3753

Bravo AF: 0.445

Asia WGS AF: 0.334 AC: 1162 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.50
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs502174; hg19: chr11-102682503;