1-217431205-TC-T

Variant names:

• chr1-217431205-TC-T
• rs796052151
• NM_018040.5:c.1526delG

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP6

The NM_018040.5(GPATCH2):​c.1526delG​(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
• Clinical Significance: Likely benign no assertion criteria provided B:1
• 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]

ACMG classification

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 rank	MANE	Protein	UniProt
GPATCH2	NM_018040.5	c.1526delG	p.Gly509AspfsTer41	frameshift_variant	Exon 10 of 10	ENST00000366935.8	NP_060510.1
GPATCH2	XM_011509689.4	c.1595delG	p.Gly532AspfsTer41	frameshift_variant	Exon 11 of 11		XP_011507991.1
GPATCH2	XM_011509690.4	c.1484delG	p.Gly495AspfsTer41	frameshift_variant	Exon 9 of 9		XP_011507992.1
GPATCH2	XM_017001592.3	c.1415delG	p.Gly472AspfsTer41	frameshift_variant	Exon 8 of 8		XP_016857081.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPATCH2	ENST00000366935.8	c.1526delG	p.Gly509AspfsTer41	frameshift_variant	Exon 10 of 10	2	NM_018040.5	ENSP00000355902.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 28

GnomAD4 genome Cov.: 33

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

Long QT syndrome Benign:1

-

Medical Research Institute, Tokyo Medical and Dental University

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: research

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs796052151; hg19: chr1-217604547;