11-102787177-C-A

Variant names:

• chr11-102787177-C-A
• rs521898
• ENST00000371455.7:n.325-10847C>A

Variant summary

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

The ENST00000525739.6(WTAPP1):​n.389+3113C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.949 in 152,162 control chromosomes in the GnomAD database, including 68,594 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 0.95 (68594 hom., cov: 30)
• Consequence: WTAPP1 ENST00000525739.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780
• Publications: 5 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.98 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000525739.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WTAPP1	NR_038390.1		n.389+3113C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WTAPP1	ENST00000371455.7	TSL:4	n.325-10847C>A		intron	N/A
	WTAPP1	ENST00000525739.6	TSL:2	n.389+3113C>A		intron	N/A
	WTAPP1	ENST00000544704.1	TSL:4	n.344+3113C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.949 AC: 144257 AN: 152044 Hom.: 68537 Cov.: 30

Gnomad AFR AF: 0.988

Gnomad AMI AF: 0.932

Gnomad AMR AF: 0.903

Gnomad ASJ AF: 0.922

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.903

Gnomad FIN AF: 0.917

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.949

Gnomad OTH AF: 0.939

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

GnomAD4 genome AF: 0.949 AC: 144373 AN: 152162 Hom.: 68594 Cov.: 30 AF XY: 0.945 AC XY: 70309 AN XY: 74374

African (AFR) AF: 0.988 AC: 41031 AN: 41522

American (AMR) AF: 0.903 AC: 13804 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.922 AC: 3198 AN: 3468

East Asian (EAS) AF: 0.894 AC: 4618 AN: 5164

South Asian (SAS) AF: 0.903 AC: 4331 AN: 4798

European-Finnish (FIN) AF: 0.917 AC: 9701 AN: 10582

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.949 AC: 64582 AN: 68026

Other (OTH) AF: 0.939 AC: 1986 AN: 2114

Alfa AF: 0.947 Hom.: 89436

Bravo AF: 0.948

Asia WGS AF: 0.910 AC: 3166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.90
DANN	Benign	0.73
PhyloP100		-0.078

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs521898;

hg19: chr11-102657908;