Variant 13-113346301-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The XM_047430838.1(LOC124903217):c.1048G>A(p.Val350Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 5/5 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0013 ( 22 hom., cov: 6)

Consequence

LOC124903217
XM_047430838.1 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.13

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 Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 13-113346301-C-T is Benign according to our data. Variant chr13-113346301-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2643989.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 22 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903217	XM_047430838.1 linkuse as main transcript	c.1048G>A	p.Val350Ile	missense_variant	2/2
GRTP1	NM_024719.4 linkuse as main transcript	c.466-1342G>A		intron_variant		ENST00000375431.9

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
GRTP1	ENST00000375431.9 linkuse as main transcript	c.466-1342G>A	intron_variant	1	NM_024719.4	P1	Q5TC63-1
GRTP1	ENST00000326039.3 linkuse as main transcript	c.232-1342G>A	intron_variant	1			Q5TC63-2
GRTP1	ENST00000375430.8 linkuse as main transcript	c.466-1342G>A	intron_variant	1			Q5TC63-3
GRTP1	ENST00000620217.4 linkuse as main transcript	c.466-1342G>A	intron_variant	2

Frequencies

GnomAD3 genomes

AF:

0.00134

AC:

AN:

46844

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000760

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00154

Gnomad ASJ

AF:

0.00393

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00171

Gnomad OTH

AF:

0.00

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

GnomAD4 genome

AF:

0.00134

AC:

AN:

46844

Hom.:

Cov.:

AF XY:

0.00134

AC XY:

AN XY:

21594

show subpopulations

Gnomad4 AFR

AF:

0.000759

Gnomad4 AMR

AF:

0.00154

Gnomad4 ASJ

AF:

0.00393

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00171

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.0106

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

Mar 01, 2023

GRTP1: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

4.6

DANN

Benign

0.93

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