rs498186

Variant names:

• chr11-102798914-A-C
• rs498186
• ENST00000371455.7:n.423+792A>C

Your query was ambiguous. Multiple possible variants found:

• chr11-102798914-A-C
• chr11-102798914-A-G

Variant summary

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

The ENST00000525739.6(WTAPP1):​n.682+792A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 152,024 control chromosomes in the GnomAD database, including 13,007 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 0.41 (13007 hom., cov: 32)
• Consequence: WTAPP1 ENST00000525739.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319
• Publications: 26 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.476 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.682+792A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WTAPP1	ENST00000371455.7	TSL:4	n.423+792A>C		intron	N/A
	WTAPP1	ENST00000525739.6	TSL:2	n.682+792A>C		intron	N/A
	WTAPP1	ENST00000544704.1	TSL:4	n.443+792A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61938 AN: 151906 Hom.: 13001 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.407 AC: 61948 AN: 152024 Hom.: 13007 Cov.: 32 AF XY: 0.412 AC XY: 30583 AN XY: 74292

African (AFR) AF: 0.282 AC: 11717 AN: 41478

American (AMR) AF: 0.485 AC: 7410 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1618 AN: 3472

East Asian (EAS) AF: 0.469 AC: 2418 AN: 5160

South Asian (SAS) AF: 0.467 AC: 2247 AN: 4812

European-Finnish (FIN) AF: 0.496 AC: 5229 AN: 10548

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29876 AN: 67962

Other (OTH) AF: 0.423 AC: 891 AN: 2108

Alfa AF: 0.434 Hom.: 46767

Bravo AF: 0.406

Asia WGS AF: 0.450 AC: 1562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.9
DANN	Benign	0.58
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs498186; hg19: chr11-102669645;