rs7926920

Variant names:

• chr11-102827993-G-A
• rs7926920
• ENST00000371455.7:n.424-2739G>A

Variant summary

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

The ENST00000525739.6(WTAPP1):​n.683-2739G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 152,008 control chromosomes in the GnomAD database, including 16,022 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 0.45 (16022 hom., cov: 32)
• Consequence: WTAPP1 ENST00000525739.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 12 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.505 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.683-2739G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WTAPP1	ENST00000371455.7	TSL:4	n.424-2739G>A		intron	N/A
	WTAPP1	ENST00000525739.6	TSL:2	n.683-2739G>A		intron	N/A
	WTAPP1	ENST00000544704.1	TSL:4	n.444-2739G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68865 AN: 151890 Hom.: 16013 Cov.: 32

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.453 AC: 68904 AN: 152008 Hom.: 16022 Cov.: 32 AF XY: 0.444 AC XY: 32987 AN XY: 74298

African (AFR) AF: 0.448 AC: 18583 AN: 41442

American (AMR) AF: 0.372 AC: 5675 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1330 AN: 3468

East Asian (EAS) AF: 0.324 AC: 1676 AN: 5178

South Asian (SAS) AF: 0.302 AC: 1458 AN: 4820

European-Finnish (FIN) AF: 0.386 AC: 4069 AN: 10544

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.510 AC: 34633 AN: 67974

Other (OTH) AF: 0.462 AC: 972 AN: 2106

Alfa AF: 0.461 Hom.: 2769

Bravo AF: 0.453

Asia WGS AF: 0.336 AC: 1170 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.56
DANN	Benign	0.54
PhyloP100		-1.1

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: rs7926920;

hg19: chr11-102698724;