GeneBe

rs1358815

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

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

PRIM2BP
intragenic

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.789

Publications

5 publications found
Variant links:
Genes affected
PRIM2BP (HGNC:55759): (primase 2B, pseudogene)

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ACMG classification

Classification was made for transcript

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 (Cadd=6.47).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637553.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt

There are no transcript annotations for this variant.

Ensembl Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
PRIM2BP
ENST00000637553.1
TSL:6
n.235-8841T>A
intron
N/A
ENSG00000290597
ENST00000649835.1
n.243-8841T>A
intron
N/A
ENSG00000290597
ENST00000812932.1
n.233-8841T>A
intron
N/A

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

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
CADD
Benign
6.5
PhyloP100
0.79

Splicing

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

Publications

Other links and lift over

dbSNP: rs1358815; API