rs1939008

Variant names:

• chr11-102785692-G-A
• rs1939008
• ENST00000371455.7:n.325-12332G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-102785692-G-A
• chr11-102785692-G-C

Variant summary

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

The ENST00000371455.7(WTAPP1):​n.325-12332G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 152,064 control chromosomes in the GnomAD database, including 5,918 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 0.27 (5918 hom., cov: 32)
• Consequence: WTAPP1 ENST00000371455.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160
• Publications: 23 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WTAPP1	NR_038390.1	n.389+1628G>A		intron_variant	Intron 1 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WTAPP1	ENST00000371455.7	n.325-12332G>A		intron_variant	Intron 2 of 4	4
WTAPP1	ENST00000525739.6	n.389+1628G>A		intron_variant	Intron 1 of 7	2
WTAPP1	ENST00000544704.1	n.344+1628G>A		intron_variant	Intron 1 of 3	4
WTAPP1	ENST00000817290.1	n.189-12332G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40603 AN: 151946 Hom.: 5900 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.267 AC: 40648 AN: 152064 Hom.: 5918 Cov.: 32 AF XY: 0.270 AC XY: 20060 AN XY: 74322

African (AFR) AF: 0.159 AC: 6605 AN: 41482

American (AMR) AF: 0.297 AC: 4536 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 728 AN: 3470

East Asian (EAS) AF: 0.536 AC: 2772 AN: 5170

South Asian (SAS) AF: 0.362 AC: 1746 AN: 4822

European-Finnish (FIN) AF: 0.276 AC: 2912 AN: 10554

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20488 AN: 67972

Other (OTH) AF: 0.252 AC: 533 AN: 2112

Alfa AF: 0.288 Hom.: 11210

Bravo AF: 0.263

Asia WGS AF: 0.383 AC: 1333 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.4
DANN	Benign	0.51
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs1939008; hg19: chr11-102656423;