rs521898

Positions:

• chr11-102787177-C-A
• chr11-102787177-C-G
• chr11-102787177-C-T

Variant summary

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

The NR_038390.1(WTAPP1):​n.389+3113C>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 0.949 in 152,162 control chromosomes in the GnomAD database, including 68,594 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 0.95 (68594 hom., cov: 30)
• Consequence: WTAPP1 NR_038390.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.98 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WTAPP1	NR_038390.1	n.389+3113C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WTAPP1	ENST00000371455.7	n.325-10847C>A		intron_variant, non_coding_transcript_variant		4
WTAPP1	ENST00000525739.6	n.389+3113C>A		intron_variant, non_coding_transcript_variant		2
WTAPP1	ENST00000544704.1	n.344+3113C>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.949 AC: 144257 AN: 152044 Hom.: 68537 Cov.: 30

Gnomad AFR AF: 0.988

Gnomad AMI AF: 0.932

Gnomad AMR AF: 0.903

Gnomad ASJ AF: 0.922

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.903

Gnomad FIN AF: 0.917

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.949

Gnomad OTH AF: 0.939

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

GnomAD4 genome AF: 0.949 AC: 144373 AN: 152162 Hom.: 68594 Cov.: 30 AF XY: 0.945 AC XY: 70309 AN XY: 74374

Gnomad4 AFR AF: 0.988

Gnomad4 AMR AF: 0.903

Gnomad4 ASJ AF: 0.922

Gnomad4 EAS AF: 0.894

Gnomad4 SAS AF: 0.903

Gnomad4 FIN AF: 0.917

Gnomad4 NFE AF: 0.949

Gnomad4 OTH AF: 0.939

Alfa AF: 0.948 Hom.: 59350

Bravo AF: 0.948

Asia WGS AF: 0.910 AC: 3166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.90
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs521898; hg19: chr11-102657908;