rs13115988

Positions:

• chr4-89247731-G-A

Variant summary

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

The NM_198281.3(GPRIN3):​c.*49C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 1,516,038 control chromosomes in the GnomAD database, including 107,174 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 0.39 (12097 hom., cov: 32)
  • Exomes 𝑓: 0.36 (95077 hom.)
• Consequence: GPRIN3 NM_198281.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750

Genes affected

GPRIN3 (HGNC:27733): (GPRIN family member 3) Predicted to be involved in neuron projection development. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPRIN3	NM_198281.3	c.*49C>T		3_prime_UTR_variant	2/2	ENST00000609438.2	NP_938022.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPRIN3	ENST00000609438.2	c.*49C>T		3_prime_UTR_variant	2/2	2	NM_198281.3	ENSP00000476603	P1
GPRIN3	ENST00000333209.4	c.*49C>T		3_prime_UTR_variant	1/1			ENSP00000328672	P1

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59111 AN: 151804 Hom.: 12069 Cov.: 32

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.378

GnomAD3 exomes AF: 0.415 AC: 81714 AN: 196954 Hom.: 18255 AF XY: 0.412 AC XY: 42921 AN XY: 104224

Gnomad AFR exome AF: 0.430

Gnomad AMR exome AF: 0.521

Gnomad ASJ exome AF: 0.265

Gnomad EAS exome AF: 0.624

Gnomad SAS exome AF: 0.576

Gnomad FIN exome AF: 0.398

Gnomad NFE exome AF: 0.328

Gnomad OTH exome AF: 0.381

GnomAD4 exome AF: 0.364 AC: 496492 AN: 1364116 Hom.: 95077 Cov.: 24 AF XY: 0.368 AC XY: 246774 AN XY: 670566

Gnomad4 AFR exome AF: 0.430

Gnomad4 AMR exome AF: 0.515

Gnomad4 ASJ exome AF: 0.259

Gnomad4 EAS exome AF: 0.637

Gnomad4 SAS exome AF: 0.557

Gnomad4 FIN exome AF: 0.408

Gnomad4 NFE exome AF: 0.334

Gnomad4 OTH exome AF: 0.369

GnomAD4 genome AF: 0.390 AC: 59181 AN: 151922 Hom.: 12097 Cov.: 32 AF XY: 0.396 AC XY: 29439 AN XY: 74266

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.572

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.385

Alfa AF: 0.321 Hom.: 3960

Bravo AF: 0.393

Asia WGS AF: 0.603 AC: 2098 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.54

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: rs13115988; hg19: chr4-90168882; COSMIC: COSV60884083;