1-217431205-TC-T
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP6
The NM_018040.5(GPATCH2):c.1526del(p.Gly509AspfsTer41) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: not found (cov: 33)
Consequence
GPATCH2
NM_018040.5 frameshift
NM_018040.5 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 7.04
Genes affected
GPATCH2 (HGNC:25499): (G-patch domain containing 2) The gene encodes a nuclear factor that may play a role in spermatogenesis and in tumor growth during breast cancer. The encoded protein contains a G-patch domain with an RNA binding motif. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2017]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 1-217431205-TC-T is Benign according to our data. Variant chr1-217431205-TC-T is described in ClinVar as [Likely_benign]. Clinvar id is 207845.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPATCH2 | NM_018040.5 | c.1526del | p.Gly509AspfsTer41 | frameshift_variant | 10/10 | ENST00000366935.8 | |
GPATCH2 | XM_011509689.4 | c.1595del | p.Gly532AspfsTer41 | frameshift_variant | 11/11 | ||
GPATCH2 | XM_011509690.4 | c.1484del | p.Gly495AspfsTer41 | frameshift_variant | 9/9 | ||
GPATCH2 | XM_017001592.3 | c.1415del | p.Gly472AspfsTer41 | frameshift_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPATCH2 | ENST00000366935.8 | c.1526del | p.Gly509AspfsTer41 | frameshift_variant | 10/10 | 2 | NM_018040.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Cov.: 28
GnomAD4 exome
Cov.:
28
GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Long QT syndrome Benign:1
Likely benign, no assertion criteria provided | research | Medical Research Institute, Tokyo Medical and Dental University | - | - - |
Computational scores
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Calibrated prediction
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Prediction
Splicing
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Calibrated prediction
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at