rs34695796

chr11-102801370-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_038390.1(WTAPP1):n.682+3248G>A 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 0.0173 in 152,238 control chromosomes in the GnomAD database, including 29 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 0.017 (29 hom., cov: 32)
• Consequence: WTAPP1 NR_038390.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.633

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=-0.88).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0173 (2635/152238) while in subpopulation NFE AF= 0.0281 (1911/68006). AF 95% confidence interval is 0.0271. There are 29 homozygotes in gnomad4. There are 1216 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 29 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WTAPP1	NR_038390.1	n.682+3248G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WTAPP1	ENST00000371455.7	n.423+3248G>A		intron_variant, non_coding_transcript_variant		4
WTAPP1	ENST00000525739.6	n.682+3248G>A		intron_variant, non_coding_transcript_variant		2
WTAPP1	ENST00000544704.1	n.443+3248G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0173 AC: 2637 AN: 152120 Hom.: 29 Cov.: 32

Gnomad AFR AF: 0.00558

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.0156

Gnomad ASJ AF: 0.00461

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0182

Gnomad FIN AF: 0.0103

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0281

Gnomad OTH AF: 0.0129

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

GnomAD4 genome AF: 0.0173 AC: 2635 AN: 152238 Hom.: 29 Cov.: 32 AF XY: 0.0163 AC XY: 1216 AN XY: 74428

Gnomad4 AFR AF: 0.00556

Gnomad4 AMR AF: 0.0155

Gnomad4 ASJ AF: 0.00461

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0183

Gnomad4 FIN AF: 0.0103

Gnomad4 NFE AF: 0.0281

Gnomad4 OTH AF: 0.0128

Alfa AF: 0.0213 Hom.: 5

Bravo AF: 0.0167

Asia WGS AF: 0.00635 AC: 22 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.59
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34695796; hg19: chr11-102672101;