rs7317038

Positions:

• chr13-113358583-C-T

Variant summary

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

The NM_024719.4(GRTP1):​c.182-3102G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 151,978 control chromosomes in the GnomAD database, including 9,227 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 0.34 (9227 hom., cov: 34)
• Consequence: GRTP1 NM_024719.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GRTP1	NM_024719.4	c.182-3102G>A		intron_variant		ENST00000375431.9
GRTP1-AS1	NR_046541.1	n.1254+2462C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRTP1	ENST00000375431.9	c.182-3102G>A		intron_variant		1	NM_024719.4	P1
GRTP1	ENST00000375430.8	c.182-3102G>A		intron_variant		1
GRTP1-AS1	ENST00000423246.1	n.156-2976C>T		intron_variant, non_coding_transcript_variant		5
GRTP1	ENST00000620217.4	c.182-3102G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51694 AN: 151860 Hom.: 9215 Cov.: 34

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.340 AC: 51736 AN: 151978 Hom.: 9227 Cov.: 34 AF XY: 0.341 AC XY: 25322 AN XY: 74266

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.607

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.330

Gnomad4 OTH AF: 0.328

Alfa AF: 0.330 Hom.: 6210

Bravo AF: 0.357

Asia WGS AF: 0.476 AC: 1653 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.88
DANN	Benign	0.50

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: rs7317038; hg19: chr13-114012898;