Variant chr13-113346252-CCG-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The XM_047430838.1(LOC124903217):c.1095_1096del(p.Gly366ProfsTer138) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0027 ( 24 hom., cov: 0)

Failed GnomAD Quality Control

Consequence

LOC124903217
XM_047430838.1 frameshift

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.423

Variant links:

Genes affected

LOC124903217 (HGNC:):

LOC124903217 links:

GRTP1 (HGNC:20310): (growth hormone regulated TBC protein 1) Predicted to enable GTPase activator activity. Predicted to be involved in activation of GTPase activity and intracellular protein transport. [provided by Alliance of Genome Resources, Apr 2022]

GRTP1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

BP6

Variant 13-113346252-CCG-C is Benign according to our data. Variant chr13-113346252-CCG-C is described in ClinVar as [Likely_benign]. Clinvar id is 2643988.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903217	XM_047430838.1 linkuse as main transcript	c.1095_1096del	p.Gly366ProfsTer138	frameshift_variant	2/2
GRTP1	NM_024719.4 linkuse as main transcript	c.466-1295_466-1294del		intron_variant		ENST00000375431.9

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
GRTP1	ENST00000375431.9 linkuse as main transcript	c.466-1295_466-1294del	intron_variant	1	NM_024719.4	P1	Q5TC63-1
GRTP1	ENST00000326039.3 linkuse as main transcript	c.232-1295_232-1294del	intron_variant	1			Q5TC63-2
GRTP1	ENST00000375430.8 linkuse as main transcript	c.466-1295_466-1294del	intron_variant	1			Q5TC63-3
GRTP1	ENST00000620217.4 linkuse as main transcript	c.466-1295_466-1294del	intron_variant	2

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

220

AN:

81112

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00180

Gnomad AMI

AF:

0.00356

Gnomad AMR

AF:

0.00262

Gnomad ASJ

AF:

0.00176

Gnomad EAS

AF:

0.000999

Gnomad SAS

AF:

0.00130

Gnomad FIN

AF:

0.00195

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00352

Gnomad OTH

AF:

0.00286

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

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00271

AC:

220

AN:

81146

Hom.:

Cov.:

AF XY:

0.00255

AC XY:

100

AN XY:

39252

show subpopulations

Gnomad4 AFR

AF:

0.00180

Gnomad4 AMR

AF:

0.00261

Gnomad4 ASJ

AF:

0.00176

Gnomad4 EAS

AF:

0.00100

Gnomad4 SAS

AF:

0.00131

Gnomad4 FIN

AF:

0.00195

Gnomad4 NFE

AF:

0.00352

Gnomad4 OTH

AF:

0.00283

Alfa

AF:

0.0162

Hom.:

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

Jan 01, 2023

GRTP1: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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