rs912007

chr13-113353572-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024719.4(GRTP1):c.340+1751A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 151,546 control chromosomes in the GnomAD database, including 11,621 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.38 (11621 hom., cov: 31)
• Consequence: GRTP1 NM_024719.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42

Genes affected

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-AS1 (HGNC:39917): (GRTP1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GRTP1	NM_024719.4	c.340+1751A>G		intron_variant		ENST00000375431.9
GRTP1-AS1	NR_046541.1	n.299-1594T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRTP1	ENST00000375431.9	c.340+1751A>G		intron_variant		1	NM_024719.4	P1
GRTP1-AS1	ENST00000423246.1	n.155+1602T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.382 AC: 57846 AN: 151426 Hom.: 11593 Cov.: 31

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.382 AC: 57934 AN: 151546 Hom.: 11621 Cov.: 31 AF XY: 0.386 AC XY: 28576 AN XY: 74062

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.695

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.355

Alfa AF: 0.353 Hom.: 17987

Bravo AF: 0.398

Asia WGS AF: 0.539 AC: 1873 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.3
Dann	Benign	0.24
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs912007; hg19: chr13-114007887;