rs495366

Variant names:

• chr11-102824377-G-A
• rs495366
• ENST00000371455.7:n.424-6355G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000371455.7(WTAPP1):​n.424-6355G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 152,014 control chromosomes in the GnomAD database, including 9,289 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 0.34 (9289 hom., cov: 32)
• Consequence: WTAPP1 ENST00000371455.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.528
• Publications: 32 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WTAPP1	NR_038390.1	n.683-6355G>A		intron_variant	Intron 4 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WTAPP1	ENST00000371455.7	n.424-6355G>A		intron_variant	Intron 3 of 4	4
WTAPP1	ENST00000525739.6	n.683-6355G>A		intron_variant	Intron 4 of 7	2
WTAPP1	ENST00000544704.1	n.444-6355G>A		intron_variant	Intron 2 of 3	4
WTAPP1	ENST00000817290.1	n.288-6355G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50876 AN: 151896 Hom.: 9261 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.335 AC: 50937 AN: 152014 Hom.: 9289 Cov.: 32 AF XY: 0.342 AC XY: 25435 AN XY: 74308

African (AFR) AF: 0.362 AC: 15002 AN: 41436

American (AMR) AF: 0.467 AC: 7141 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1237 AN: 3472

East Asian (EAS) AF: 0.600 AC: 3107 AN: 5176

South Asian (SAS) AF: 0.550 AC: 2649 AN: 4816

European-Finnish (FIN) AF: 0.269 AC: 2836 AN: 10562

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.263 AC: 17881 AN: 67956

Other (OTH) AF: 0.336 AC: 710 AN: 2110

Alfa AF: 0.294 Hom.: 25145

Bravo AF: 0.350

Asia WGS AF: 0.531 AC: 1847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.67
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs495366; hg19: chr11-102695108;