Variant 13-113346217-TGTGGCTGA-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The XM_047430838.1(LOC124903217):c.1124_1131del(p.Leu375GlnfsTer127) 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 0.0021 ( 19 hom., cov: 0)

Consequence

LOC124903217
XM_047430838.1 frameshift

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0820

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 -6 ACMG points.

BP6

Variant 13-113346217-TGTGGCTGA-T is Benign according to our data. Variant chr13-113346217-TGTGGCTGA-T is described in ClinVar as [Likely_benign]. Clinvar id is 2643986.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 19 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903217	XM_047430838.1 linkuse as main transcript	c.1124_1131del	p.Leu375GlnfsTer127	frameshift_variant	2/2
GRTP1	NM_024719.4 linkuse as main transcript	c.466-1266_466-1259del		intron_variant		ENST00000375431.9

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
GRTP1	ENST00000375431.9 linkuse as main transcript	c.466-1266_466-1259del	intron_variant	1	NM_024719.4	P1	Q5TC63-1
GRTP1	ENST00000326039.3 linkuse as main transcript	c.232-1266_232-1259del	intron_variant	1			Q5TC63-2
GRTP1	ENST00000375430.8 linkuse as main transcript	c.466-1266_466-1259del	intron_variant	1			Q5TC63-3
GRTP1	ENST00000620217.4 linkuse as main transcript	c.466-1266_466-1259del	intron_variant	2

Frequencies

GnomAD3 genomes

AF:

0.00207

AC:

276

AN:

133044

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000402

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000765

Gnomad ASJ

AF:

0.00935

Gnomad EAS

AF:

0.000650

Gnomad SAS

AF:

0.000503

Gnomad FIN

AF:

0.00694

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00243

Gnomad OTH

AF:

0.00277

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

GnomAD4 genome

AF:

0.00207

AC:

276

AN:

133118

Hom.:

Cov.:

AF XY:

0.00202

AC XY:

131

AN XY:

64868

show subpopulations

Gnomad4 AFR

AF:

0.000401

Gnomad4 AMR

AF:

0.000764

Gnomad4 ASJ

AF:

0.00935

Gnomad4 EAS

AF:

0.000652

Gnomad4 SAS

AF:

0.000505

Gnomad4 FIN

AF:

0.00694

Gnomad4 NFE

AF:

0.00243

Gnomad4 OTH

AF:

0.00274

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

GRTP1: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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.