11-102834927-C-G

Position:

• chr11-102834927-C-G

Variant summary

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

The NR_038390.1(WTAPP1):​n.2313+1363C>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 0.349 in 152,082 control chromosomes in the GnomAD database, including 10,104 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 0.35 (10104 hom., cov: 32)
• Consequence: WTAPP1 NR_038390.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WTAPP1	NR_038390.1	n.2313+1363C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WTAPP1	ENST00000525739.6	n.2313+1363C>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52940 AN: 151964 Hom.: 10073 Cov.: 32

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.349 AC: 53009 AN: 152082 Hom.: 10104 Cov.: 32 AF XY: 0.355 AC XY: 26396 AN XY: 74342

Gnomad4 AFR AF: 0.409

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.600

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.347

Alfa AF: 0.167 Hom.: 331

Bravo AF: 0.366

Asia WGS AF: 0.537 AC: 1865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs683878; hg19: chr11-102705658;