13-113346301-C-T

Position:

• chr13-113346301-C-T

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.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
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.13

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=-0.83).
• 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	Protein	UniProt
LOC124903217	XM_047430838.1	c.1048G>A	p.Val350Ile	missense_variant	2/2		XP_047286794.1
GRTP1	NM_024719.4	c.466-1342G>A		intron_variant		ENST00000375431.9	NP_078995.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GRTP1	ENST00000375431.9	c.466-1342G>A		intron_variant		1	NM_024719.4	ENSP00000364580	P1
GRTP1	ENST00000326039.3	c.232-1342G>A		intron_variant		1		ENSP00000321850
GRTP1	ENST00000375430.8	c.466-1342G>A		intron_variant		1		ENSP00000364579
GRTP1	ENST00000620217.4	c.466-1342G>A		intron_variant		2		ENSP00000483734

Frequencies

GnomAD3 genomes AF: 0.00134 AC: 63 AN: 46844 Hom.: 22 Cov.: 6

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: 63 AN: 46844 Hom.: 22 Cov.: 6 AF XY: 0.00134 AC XY: 29 AN XY: 21594

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.: 2

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

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

Other links and lift over

dbSNP: rs1424383651; hg19: chr13-114000616;