13-113346176-G-A

Position:

• chr13-113346176-G-A

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_Strong BP6_Moderate BP7 BS2

The XM_047430838.1(LOC124903217):​c.1173C>T​(p.Pro391=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00264 in 130,734 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: 𝑓 0.0026 (7 hom., cov: 28)
• Consequence: LOC124903217 XM_047430838.1 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.649

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 -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 13-113346176-G-A is Benign according to our data. Variant chr13-113346176-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2643985.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-0.649 with no splicing effect.
• BS2: High Homozygotes in GnomAd4 at 7 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903217	XM_047430838.1	c.1173C>T	p.Pro391=	synonymous_variant	2/2
GRTP1	NM_024719.4	c.466-1217C>T		intron_variant		ENST00000375431.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRTP1	ENST00000375431.9	c.466-1217C>T		intron_variant		1	NM_024719.4	P1
GRTP1	ENST00000326039.3	c.232-1217C>T		intron_variant		1
GRTP1	ENST00000375430.8	c.466-1217C>T		intron_variant		1
GRTP1	ENST00000620217.4	c.466-1217C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.00262 AC: 342 AN: 130666 Hom.: 6 Cov.: 28

Gnomad AFR AF: 0.00876

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00108

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00303

Gnomad SAS AF: 0.000952

Gnomad FIN AF: 0.000436

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000414

Gnomad OTH AF: 0.00339

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

GnomAD4 genome AF: 0.00264 AC: 345 AN: 130734 Hom.: 7 Cov.: 28 AF XY: 0.00266 AC XY: 169 AN XY: 63576

Gnomad4 AFR AF: 0.00883

Gnomad4 AMR AF: 0.00108

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00303

Gnomad4 SAS AF: 0.000953

Gnomad4 FIN AF: 0.000436

Gnomad4 NFE AF: 0.000414

Gnomad4 OTH AF: 0.00336

Alfa AF: 0.00877 Hom.: 1

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

Dec 01, 2023

GRTP1: BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.5
DANN	Benign	0.58

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

Other links and lift over

dbSNP: rs1208297502; hg19: chr13-114000491;