rs2155013

Positions:

• chr11-102831127-T-C

Variant summary

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

The NR_038390.1(WTAPP1):​n.761+317T>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 0.447 in 151,972 control chromosomes in the GnomAD database, including 15,569 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 0.45 (15569 hom., cov: 31)
• Consequence: WTAPP1 NR_038390.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.411

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WTAPP1	NR_038390.1	n.761+317T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WTAPP1	ENST00000371455.7	n.502+317T>C		intron_variant, non_coding_transcript_variant		4
WTAPP1	ENST00000525739.6	n.761+317T>C		intron_variant, non_coding_transcript_variant		2
WTAPP1	ENST00000544704.1	n.522+317T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67889 AN: 151854 Hom.: 15566 Cov.: 31

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.447 AC: 67917 AN: 151972 Hom.: 15569 Cov.: 31 AF XY: 0.438 AC XY: 32530 AN XY: 74298

Gnomad4 AFR AF: 0.423

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.456

Alfa AF: 0.462 Hom.: 2584

Bravo AF: 0.445

Asia WGS AF: 0.336 AC: 1170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.7
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2155013; hg19: chr11-102701858;