rs912007

Variant names:

• chr13-113353572-T-C
• rs912007
• NM_024719.4:c.340+1751A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000375431.9(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 ENST00000375431.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000375431.9. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GRTP1	NM_024719.4	MANE Select	c.340+1751A>G		intron	N/A	NP_078995.2
	GRTP1	NM_001286732.2		c.340+1751A>G		intron	N/A	NP_001273661.1
	GRTP1	NM_001411029.1		c.106+1751A>G		intron	N/A	NP_001397958.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GRTP1	ENST00000375431.9	TSL:1 MANE Select	c.340+1751A>G		intron	N/A	ENSP00000364580.3
	GRTP1	ENST00000375430.8	TSL:1	c.340+1751A>G		intron	N/A	ENSP00000364579.4
	GRTP1	ENST00000326039.3	TSL:1	c.106+1751A>G		intron	N/A	ENSP00000321850.3

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

African (AFR) AF: 0.428 AC: 17631 AN: 41228

American (AMR) AF: 0.432 AC: 6591 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 978 AN: 3466

East Asian (EAS) AF: 0.695 AC: 3583 AN: 5154

South Asian (SAS) AF: 0.399 AC: 1910 AN: 4786

European-Finnish (FIN) AF: 0.340 AC: 3573 AN: 10494

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22637 AN: 67874

Other (OTH) AF: 0.355 AC: 743 AN: 2092

Alfa AF: 0.354 Hom.: 23879

Bravo AF: 0.398

Asia WGS AF: 0.539 AC: 1873 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.24
PhyloP100		-2.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs912007; hg19: chr13-114007887;