11-102814204-T-G

Position:

• chr11-102814204-T-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+16082T>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 0.383 in 152,022 control chromosomes in the GnomAD database, including 12,264 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 0.38 (12264 hom., cov: 32)
• Consequence: WTAPP1 NR_038390.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WTAPP1	NR_038390.1	n.682+16082T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WTAPP1	ENST00000371455.7	n.423+16082T>G		intron_variant, non_coding_transcript_variant		4
WTAPP1	ENST00000525739.6	n.682+16082T>G		intron_variant, non_coding_transcript_variant		2
WTAPP1	ENST00000544704.1	n.443+16082T>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58193 AN: 151904 Hom.: 12227 Cov.: 32

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.383 AC: 58275 AN: 152022 Hom.: 12264 Cov.: 32 AF XY: 0.388 AC XY: 28865 AN XY: 74300

Gnomad4 AFR AF: 0.495

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.597

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.370

Alfa AF: 0.333 Hom.: 1135

Bravo AF: 0.403

Asia WGS AF: 0.549 AC: 1907 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.82
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1144398; hg19: chr11-102684935;