rs473509

Variant names:

• chr11-102798998-C-G
• rs473509
• ENST00000371455.7:n.423+876C>G

Your query was ambiguous. Multiple possible variants found:

• chr11-102798998-C-G
• chr11-102798998-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000371455.7(WTAPP1):​n.423+876C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: WTAPP1 ENST00000371455.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.492
• Publications: 11 publications found

Genes affected

WTAPP1 (HGNC:):

WTAPP1 (HGNC:44115): (WTAP pseudogene 1)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WTAPP1	NR_038390.1	n.682+876C>G		intron_variant	Intron 4 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WTAPP1	ENST00000371455.7	n.423+876C>G		intron_variant	Intron 3 of 4	4
WTAPP1	ENST00000525739.6	n.682+876C>G		intron_variant	Intron 4 of 7	2
WTAPP1	ENST00000544704.1	n.443+876C>G		intron_variant	Intron 2 of 3	4
WTAPP1	ENST00000817290.1	n.287+876C>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 793

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.31
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs473509; hg19: chr11-102669729;