chr11-102834166-A-G

Variant names:

• chr11-102834166-A-G
• rs595840
• ENST00000525739.6:n.2313+602A>G

Variant summary

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

The ENST00000525739.6(WTAPP1):​n.2313+602A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 151,964 control chromosomes in the GnomAD database, including 25,449 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 0.57 (25449 hom., cov: 32)
• Consequence: WTAPP1 ENST00000525739.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251
• Publications: 11 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.678 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.2313+602A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WTAPP1	ENST00000525739.6	TSL:2	n.2313+602A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86927 AN: 151846 Hom.: 25410 Cov.: 32

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.573 AC: 87023 AN: 151964 Hom.: 25449 Cov.: 32 AF XY: 0.581 AC XY: 43145 AN XY: 74262

African (AFR) AF: 0.644 AC: 26700 AN: 41446

American (AMR) AF: 0.637 AC: 9735 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2132 AN: 3470

East Asian (EAS) AF: 0.676 AC: 3492 AN: 5164

South Asian (SAS) AF: 0.698 AC: 3365 AN: 4822

European-Finnish (FIN) AF: 0.606 AC: 6366 AN: 10510

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33363 AN: 67960

Other (OTH) AF: 0.555 AC: 1172 AN: 2110

Alfa AF: 0.505 Hom.: 13695

Bravo AF: 0.578

Asia WGS AF: 0.667 AC: 2318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.27
DANN	Benign	0.71
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs595840; hg19: chr11-102704897;