rs7317038

Variant names:

• chr13-113358583-C-T
• rs7317038
• NM_024719.4:c.182-3102G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 26 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=-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 rank	MANE	Protein	UniProt
GRTP1	NM_024719.4	c.182-3102G>A		intron_variant	Intron 2 of 7	ENST00000375431.9	NP_078995.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GRTP1	ENST00000375431.9	c.182-3102G>A		intron_variant	Intron 2 of 7	1	NM_024719.4	ENSP00000364580.3

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

African (AFR) AF: 0.312 AC: 12927 AN: 41414

American (AMR) AF: 0.442 AC: 6744 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 881 AN: 3470

East Asian (EAS) AF: 0.607 AC: 3147 AN: 5184

South Asian (SAS) AF: 0.360 AC: 1736 AN: 4818

European-Finnish (FIN) AF: 0.282 AC: 2969 AN: 10532

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.330 AC: 22398 AN: 67972

Other (OTH) AF: 0.328 AC: 693 AN: 2114

Alfa AF: 0.335 Hom.: 25285

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
PhyloP100		-0.22
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: rs7317038; hg19: chr13-114012898;