GeneBe

ENST00000646873.1:c.312-12773G>C

Variant names:

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_005049.3(PWP2):​c.2141-363C>. variant causes a intron change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 N/A ( N/A hom., cov: )
Exomes 𝑓: N/A ( N/A hom. )

Consequence

PWP2
NM_005049.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

No conservation score assigned
Variant links:
Genes affected
PWP2 (HGNC:9711): (PWP2 small subunit processome component) Enables RNA binding activity. Predicted to be involved in maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) and ribosomal small subunit assembly. Predicted to be located in nucleoplasm. Predicted to be part of Pwp2p-containing subcomplex of 90S preribosome and small-subunit processome. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PWP2NM_005049.3 linkc.2141-363C>. intron_variant Intron 17 of 20 ENST00000291576.12 NP_005040.2 Q15269

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PWP2ENST00000291576.12 linkc.2141-363C>. intron_variant Intron 17 of 20 1 NM_005049.3 ENSP00000291576.6 Q15269
PWP2ENST00000471490.1 linkn.4278C>. non_coding_transcript_exon_variant Exon 6 of 6 2
PWP2ENST00000494310.5 linkn.176-6C>. splice_region_variant, intron_variant Intron 2 of 5 5
PWP2ENST00000476948.1 linkn.-230C>. upstream_gene_variant 3

Frequencies

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

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr21-45547450; API