11-102831153-G-A

Variant names:

• chr11-102831153-G-A
• rs527832
• ENST00000371455.7:n.503-315G>A

Variant summary

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

The ENST00000371455.7(WTAPP1):​n.503-315G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0786 in 152,188 control chromosomes in the GnomAD database, including 603 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 0.079 (603 hom., cov: 33)
• Consequence: WTAPP1 ENST00000371455.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238
• Publications: 8 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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000371455.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WTAPP1	NR_038390.1		n.762-315G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WTAPP1	ENST00000371455.7	TSL:4	n.503-315G>A		intron	N/A
	WTAPP1	ENST00000525739.6	TSL:2	n.762-315G>A		intron	N/A
	WTAPP1	ENST00000544704.1	TSL:4	n.522+343G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0788 AC: 11978 AN: 152070 Hom.: 602 Cov.: 33

Gnomad AFR AF: 0.0223

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0819

Gnomad ASJ AF: 0.0533

Gnomad EAS AF: 0.0548

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.0677

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.0773

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

GnomAD4 genome AF: 0.0786 AC: 11967 AN: 152188 Hom.: 603 Cov.: 33 AF XY: 0.0777 AC XY: 5783 AN XY: 74398

African (AFR) AF: 0.0223 AC: 926 AN: 41540

American (AMR) AF: 0.0818 AC: 1250 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0533 AC: 185 AN: 3468

East Asian (EAS) AF: 0.0547 AC: 283 AN: 5172

South Asian (SAS) AF: 0.199 AC: 960 AN: 4818

European-Finnish (FIN) AF: 0.0677 AC: 717 AN: 10592

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7439 AN: 68002

Other (OTH) AF: 0.0764 AC: 161 AN: 2106

Alfa AF: 0.0914 Hom.: 801

Bravo AF: 0.0762

Asia WGS AF: 0.113 AC: 394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.6
DANN	Benign	0.28
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs527832; hg19: chr11-102701884;