11-102798581-A-T

Position:

• chr11-102798581-A-T

Variant summary

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

The NR_038390.1(WTAPP1):​n.682+459A>T 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 0.478 in 151,862 control chromosomes in the GnomAD database, including 17,763 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 0.48 (17763 hom., cov: 31)
• Consequence: WTAPP1 NR_038390.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.555

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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WTAPP1	NR_038390.1	n.682+459A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WTAPP1	ENST00000371455.7	n.423+459A>T		intron_variant, non_coding_transcript_variant		4
WTAPP1	ENST00000525739.6	n.682+459A>T		intron_variant, non_coding_transcript_variant		2
WTAPP1	ENST00000544704.1	n.443+459A>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72493 AN: 151746 Hom.: 17724 Cov.: 31

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.478 AC: 72601 AN: 151862 Hom.: 17763 Cov.: 31 AF XY: 0.478 AC XY: 35448 AN XY: 74206

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.652

Gnomad4 SAS AF: 0.652

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.460

Alfa AF: 0.305 Hom.: 706

Bravo AF: 0.480

Asia WGS AF: 0.643 AC: 2236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.73
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs475007; hg19: chr11-102669312;