4-89304684-T-C

Variant names:

• chr4-89304684-T-C
• rs1560488
• NM_198281.3:c.-124+2931A>G

Variant summary

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

The NM_198281.3(GPRIN3):​c.-124+2931A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.797 in 152,092 control chromosomes in the GnomAD database, including 48,557 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 0.80 (48557 hom., cov: 31)
• Consequence: GPRIN3 NM_198281.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPRIN3	NM_198281.3	c.-124+2931A>G		intron_variant	Intron 1 of 1	ENST00000609438.2	NP_938022.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPRIN3	ENST00000609438.2	c.-124+2931A>G		intron_variant	Intron 1 of 1	2	NM_198281.3	ENSP00000476603.1

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121201 AN: 151974 Hom.: 48520 Cov.: 31

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.896

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.797 AC: 121292 AN: 152092 Hom.: 48557 Cov.: 31 AF XY: 0.804 AC XY: 59748 AN XY: 74350

Gnomad4 AFR AF: 0.801

Gnomad4 AMR AF: 0.828

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.895

Gnomad4 FIN AF: 0.808

Gnomad4 NFE AF: 0.767

Gnomad4 OTH AF: 0.787

Alfa AF: 0.773 Hom.: 52929

Bravo AF: 0.799

Asia WGS AF: 0.934 AC: 3247 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.25
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: rs1560488; hg19: chr4-90225835;