11-102834166-A-G

Position:

• chr11-102834166-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.2313+602A>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 0.573 in 151,964 control chromosomes in the GnomAD database, including 25,449 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 0.57 (25449 hom., cov: 32)
• Consequence: WTAPP1 NR_038390.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251

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=-0.93).
• 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	UniProt
WTAPP1	NR_038390.1	n.2313+602A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WTAPP1	ENST00000525739.6	n.2313+602A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86927 AN: 151846 Hom.: 25410 Cov.: 32

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.573 AC: 87023 AN: 151964 Hom.: 25449 Cov.: 32 AF XY: 0.581 AC XY: 43145 AN XY: 74262

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.637

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.698

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.555

Alfa AF: 0.497 Hom.: 9593

Bravo AF: 0.578

Asia WGS AF: 0.667 AC: 2318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.27
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs595840; hg19: chr11-102704897;