ENST00000371455.7:n.325-13698A>G

Variant names:

• chr11-102784326-A-G
• rs7127735
• ENST00000371455.7:n.325-13698A>G

Variant summary

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

The ENST00000371455.7(WTAPP1):​n.325-13698A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,294 control chromosomes in the GnomAD database, including 1,446 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 0.12 (1446 hom., cov: 33)
• Consequence: WTAPP1 ENST00000371455.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.232 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WTAPP1	NR_038390.1		n.389+262A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WTAPP1	ENST00000371455.7	TSL:4	n.325-13698A>G		intron	N/A
	WTAPP1	ENST00000525739.6	TSL:2	n.389+262A>G		intron	N/A
	WTAPP1	ENST00000544704.1	TSL:4	n.344+262A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18243 AN: 152176 Hom.: 1442 Cov.: 33

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.0348

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0722

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.120 AC: 18254 AN: 152294 Hom.: 1446 Cov.: 33 AF XY: 0.121 AC XY: 9020 AN XY: 74482

African (AFR) AF: 0.179 AC: 7440 AN: 41562

American (AMR) AF: 0.182 AC: 2776 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 479 AN: 3468

East Asian (EAS) AF: 0.244 AC: 1262 AN: 5180

South Asian (SAS) AF: 0.124 AC: 598 AN: 4832

European-Finnish (FIN) AF: 0.0348 AC: 370 AN: 10624

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0722 AC: 4913 AN: 68014

Other (OTH) AF: 0.144 AC: 305 AN: 2114

Alfa AF: 0.112 Hom.: 704

Bravo AF: 0.133

Asia WGS AF: 0.209 AC: 726 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	0.64
DANN	Benign	0.44
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs7127735; hg19: chr11-102655057;