3-14493710-G-T

Position:

• chr3-14493710-G-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001080423.4(GRIP2):​c.3087C>A​(p.Ser1029Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 10/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: GRIP2 NM_001080423.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.0460

Genes affected

GRIP2 (HGNC:23841): (glutamate receptor interacting protein 2) Predicted to enable protein C-terminus binding activity. Predicted to be involved in several processes, including neurotransmitter receptor transport, endosome to postsynaptic membrane; positive regulation of AMPA glutamate receptor clustering; and positive regulation of excitatory postsynaptic potential. Predicted to act upstream of or within Notch signaling pathway; artery smooth muscle contraction; and positive regulation of blood pressure. Predicted to be located in cytoplasm; dendritic shaft; and neuron spine. Predicted to be active in glutamatergic synapse and postsynaptic density. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.06759763).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GRIP2	NM_001080423.4	c.3087C>A	p.Ser1029Arg	missense_variant	24/24	ENST00000621039.5	NP_001073892.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GRIP2	ENST00000621039.5	c.3087C>A	p.Ser1029Arg	missense_variant	24/24	1	NM_001080423.4	ENSP00000478352	P2
GRIP2	ENST00000619221.4	c.3378C>A	p.Ser1126Arg	missense_variant	25/25	5		ENSP00000480660
GRIP2	ENST00000637182.1	c.3102C>A	p.Ser1034Arg	missense_variant	24/24	5		ENSP00000490949	A1
GRIP2	ENST00000430219.2	c.*747C>A		3_prime_UTR_variant, NMD_transcript_variant	12/12	2		ENSP00000481670

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jun 21, 2022

The c.3378C>A (p.S1126R) alteration is located in exon 25 (coding exon 25) of the GRIP2 gene. This alteration results from a C to A substitution at nucleotide position 3378, causing the serine (S) at amino acid position 1126 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Benign	-0.076	T
BayesDel_noAF	Benign	-0.35
CADD	Benign	3.6
DANN	Benign	0.86
DEOGEN2	Benign	0.058	T;.;.
FATHMM_MKL	Benign	0.12	N
LIST_S2	Benign	0.57	T;T;T
MetaRNN	Benign	0.068	T;T;T
MutationAssessor	Benign	-0.32	N;.;.
PrimateAI	Benign	0.38	T
Sift4G	Benign	0.34	T;T;.
Polyphen		0.0	B;.;.
Vest4		0.17
MVP		0.68
GERP RS		1.6
Varity_R		0.035
gMVP		0.28

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr3-14535218; COSMIC: COSV56120616; COSMIC: COSV56120616;