rs34695796

Variant names:

• chr11-102801370-G-A
• rs34695796
• ENST00000371455.7:n.423+3248G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000371455.7(WTAPP1):​n.423+3248G>A variant causes a intron 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 ENST00000371455.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.633
• Publications: 1 publications found

Genes affected

WTAPP1 (HGNC:):

WTAPP1 (HGNC:44115): (WTAP pseudogene 1)

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 29 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WTAPP1	NR_038390.1	n.682+3248G>A		intron_variant	Intron 4 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WTAPP1	ENST00000371455.7	n.423+3248G>A		intron_variant	Intron 3 of 4	4
WTAPP1	ENST00000525739.6	n.682+3248G>A		intron_variant	Intron 4 of 7	2
WTAPP1	ENST00000544704.1	n.443+3248G>A		intron_variant	Intron 2 of 3	4
WTAPP1	ENST00000817290.1	n.287+3248G>A		intron_variant	Intron 3 of 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

African (AFR) AF: 0.00556 AC: 231 AN: 41552

American (AMR) AF: 0.0155 AC: 237 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.00461 AC: 16 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5174

South Asian (SAS) AF: 0.0183 AC: 88 AN: 4818

European-Finnish (FIN) AF: 0.0103 AC: 109 AN: 10614

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0281 AC: 1911 AN: 68006

Other (OTH) AF: 0.0128 AC: 27 AN: 2116

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
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs34695796; hg19: chr11-102672101;