Variant 1-217620142-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_018040.5(GPATCH2):c.414G>A(p.Gly138=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00783 in 1,614,044 control chromosomes in the GnomAD database, including 80 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0059 ( 6 hom., cov: 32)

Exomes 𝑓: 0.0080 ( 74 hom. )

Consequence

GPATCH2
NM_018040.5 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0800

Variant links:

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]

GPATCH2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.34).

BP6

Variant 1-217620142-C-T is Benign according to our data. Variant chr1-217620142-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2639900.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.08 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPATCH2	NM_018040.5 linkuse as main transcript	c.414G>A	p.Gly138=	synonymous_variant	2/10	ENST00000366935.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPATCH2	ENST00000366935.8 linkuse as main transcript	c.414G>A	p.Gly138=	synonymous_variant	2/10	2	NM_018040.5	P1	Q9NW75-1
GPATCH2	ENST00000366934.3 linkuse as main transcript	c.414G>A	p.Gly138=	synonymous_variant	2/6	1			Q9NW75-2

Frequencies

GnomAD3 genomes

AF:

0.00592

AC:

900

AN:

152154

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00116

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00484

Gnomad ASJ

AF:

0.00317

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00934

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00957

Gnomad OTH

AF:

0.00766

GnomAD3 exomes

AF:

0.00610

AC:

1530

AN:

250926

Hom.:

AF XY:

0.00595

AC XY:

807

AN XY:

135602

show subpopulations

Gnomad AFR exome

AF:

0.00129

Gnomad AMR exome

AF:

0.00257

Gnomad ASJ exome

AF:

0.00199

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000196

Gnomad FIN exome

AF:

0.0103

Gnomad NFE exome

AF:

0.0100

Gnomad OTH exome

AF:

0.00604

GnomAD4 exome

AF:

0.00803

AC:

11745

AN:

1461772

Hom.:

Cov.:

AF XY:

0.00785

AC XY:

5706

AN XY:

727198

show subpopulations

Gnomad4 AFR exome

AF:

0.00128

Gnomad4 AMR exome

AF:

0.00264

Gnomad4 ASJ exome

AF:

0.00275

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000301

Gnomad4 FIN exome

AF:

0.0108

Gnomad4 NFE exome

AF:

0.00941

Gnomad4 OTH exome

AF:

0.00722

GnomAD4 genome

AF:

0.00590

AC:

899

AN:

152272

Hom.:

Cov.:

AF XY:

0.00602

AC XY:

448

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.00116

Gnomad4 AMR

AF:

0.00484

Gnomad4 ASJ

AF:

0.00317

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00934

Gnomad4 NFE

AF:

0.00957

Gnomad4 OTH

AF:

0.00758

Alfa

AF:

0.00849

Hom.:

Bravo

AF:

0.00534

EpiCase

AF:

0.00851

EpiControl

AF:

0.00794

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Nov 01, 2022

GPATCH2: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.34

CADD

Benign

4.0

DANN

Benign

0.54

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over