11-102832897-A-G

Position:

• chr11-102832897-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.2191A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 151,920 control chromosomes in the GnomAD database, including 23,056 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 0.55 (23056 hom., cov: 31)
  • Exomes 𝑓: 0.33 (0 hom.)
• Consequence: WTAPP1 NR_038390.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.507

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=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WTAPP1	NR_038390.1	n.2191A>G		non_coding_transcript_exon_variant	6/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WTAPP1	ENST00000525739.6	n.2191A>G		non_coding_transcript_exon_variant	6/8	2

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82928 AN: 151790 Hom.: 23023 Cov.: 31

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.538

GnomAD4 exome AF: 0.333 AC: 4 AN: 12 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 3 AN XY: 6

Gnomad4 NFE exome AF: 0.333

GnomAD4 genome AF: 0.546 AC: 83014 AN: 151908 Hom.: 23056 Cov.: 31 AF XY: 0.556 AC XY: 41252 AN XY: 74254

Gnomad4 AFR AF: 0.553

Gnomad4 AMR AF: 0.629

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.677

Gnomad4 SAS AF: 0.697

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.490

Gnomad4 OTH AF: 0.539

Alfa AF: 0.521 Hom.: 2575

Bravo AF: 0.547

Asia WGS AF: 0.663 AC: 2303 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	1.6
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs635746; hg19: chr11-102703628;