chr13-113346103-C-A

Position:

• chr13-113346103-C-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The XM_047430838.1(LOC124903217):​c.1246G>T​(p.Gly416Cys) 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 0.0048 (3 hom., cov: 3)
• Consequence: LOC124903217 XM_047430838.1 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.394

Genes affected

LOC124903217 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 13-113346103-C-A is Benign according to our data. Variant chr13-113346103-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2643984.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903217	XM_047430838.1	c.1246G>T	p.Gly416Cys	missense_variant	2/2
GRTP1	NM_024719.4	c.466-1144G>T		intron_variant		ENST00000375431.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRTP1	ENST00000375431.9	c.466-1144G>T		intron_variant		1	NM_024719.4	P1
GRTP1	ENST00000326039.3	c.232-1144G>T		intron_variant		1
GRTP1	ENST00000375430.8	c.466-1144G>T		intron_variant		1
GRTP1	ENST00000620217.4	c.466-1144G>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.00483 AC: 220 AN: 45580 Hom.: 3 Cov.: 3

Gnomad AFR AF: 0.00422

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00227

Gnomad ASJ AF: 0.00327

Gnomad EAS AF: 0.00103

Gnomad SAS AF: 0.00464

Gnomad FIN AF: 0.00230

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00633

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.00482 AC: 220 AN: 45598 Hom.: 3 Cov.: 3 AF XY: 0.00441 AC XY: 96 AN XY: 21754

Gnomad4 AFR AF: 0.00421

Gnomad4 AMR AF: 0.00227

Gnomad4 ASJ AF: 0.00327

Gnomad4 EAS AF: 0.00103

Gnomad4 SAS AF: 0.00469

Gnomad4 FIN AF: 0.00230

Gnomad4 NFE AF: 0.00633

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

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
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.9
DANN	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs61966590; hg19: chr13-114000418;