chr9-101570213-A-C

Variant names:

• chr9-101570213-A-C
• rs7030238
• NM_133445.3:c.*2961T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_133445.3(GRIN3A):​c.*2961T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 151,998 control chromosomes in the GnomAD database, including 4,868 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 0.25 (4867 hom., cov: 32)
  • Exomes 𝑓: 0.20 (1 hom.)
• Consequence: GRIN3A NM_133445.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211
• Publications: 10 publications found

Genes affected

GRIN3A (HGNC:16767): (glutamate ionotropic receptor NMDA type subunit 3A) This gene encodes a subunit of the N-methyl-D-aspartate (NMDA) receptors, which belong to the superfamily of glutamate-regulated ion channels, and function in physiological and pathological processes in the central nervous system. This subunit shows greater than 90% identity to the corresponding subunit in rat. Studies in the knockout mouse deficient in this subunit suggest that this gene may be involved in the development of synaptic elements by modulating NMDA receptor activity. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_133445.3. 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
	GRIN3A	NM_133445.3	MANE Select	c.*2961T>G		3_prime_UTR	Exon 9 of 9	NP_597702.2	Q8TCU5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GRIN3A	ENST00000361820.6	TSL:1 MANE Select	c.*2961T>G		3_prime_UTR	Exon 9 of 9	ENSP00000355155.3	Q8TCU5

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37771 AN: 151814 Hom.: 4868 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.257

GnomAD4 exome AF: 0.197 AC: 13 AN: 66 Hom.: 1 Cov.: 0 AF XY: 0.114 AC XY: 5 AN XY: 44

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.200 AC: 12 AN: 60

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 1 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.249 AC: 37781 AN: 151932 Hom.: 4867 Cov.: 32 AF XY: 0.243 AC XY: 18067 AN XY: 74246

African (AFR) AF: 0.304 AC: 12584 AN: 41390

American (AMR) AF: 0.257 AC: 3916 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 746 AN: 3472

East Asian (EAS) AF: 0.238 AC: 1226 AN: 5158

South Asian (SAS) AF: 0.171 AC: 827 AN: 4824

European-Finnish (FIN) AF: 0.184 AC: 1942 AN: 10542

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15697 AN: 67970

Other (OTH) AF: 0.254 AC: 536 AN: 2112

Alfa AF: 0.233 Hom.: 2928

Bravo AF: 0.262

Asia WGS AF: 0.225 AC: 782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.86
DANN	Benign	0.37
PhyloP100		-0.21
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs7030238; hg19: chr9-104332495; COSMIC: COSV62451955;