4-89304684-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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]

ENSG00000297652 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198281.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPRIN3	NM_198281.3	MANE Select	c.-124+2931A>G		intron	N/A	NP_938022.2	Q6ZVF9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPRIN3	ENST00000609438.2	TSL:2 MANE Select	c.-124+2931A>G		intron	N/A	ENSP00000476603.1	Q6ZVF9
	GPRIN3	ENST00000715382.1		c.-124+2931A>G		intron	N/A	ENSP00000520450.1	Q6ZVF9
	GPRIN3	ENST00000901096.1		c.-124+2178A>G		intron	N/A	ENSP00000571155.1

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

African (AFR) AF: 0.801 AC: 33192 AN: 41450

American (AMR) AF: 0.828 AC: 12666 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.779 AC: 2704 AN: 3472

East Asian (EAS) AF: 0.995 AC: 5153 AN: 5180

South Asian (SAS) AF: 0.895 AC: 4315 AN: 4820

European-Finnish (FIN) AF: 0.808 AC: 8544 AN: 10574

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.767 AC: 52139 AN: 67996

Other (OTH) AF: 0.787 AC: 1657 AN: 2106

Alfa AF: 0.778 Hom.: 69528

Bravo AF: 0.799

Asia WGS AF: 0.934 AC: 3247 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.25
DANN	Benign	0.50
PhyloP100		-1.6
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: rs1560488; hg19: chr4-90225835;