NM_152495.2:c.82-2870C>G

Variant names:

• chr1-224678088-C-G
• rs930323
• NM_152495.2:c.82-2870C>G

Variant summary

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

The NM_152495.2(CNIH3):​c.82-2870C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 151,994 control chromosomes in the GnomAD database, including 3,212 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 0.19 (3212 hom., cov: 32)
• Consequence: CNIH3 NM_152495.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260
• Publications: 5 publications found

Genes affected

CNIH3 (HGNC:26802): (cornichon family AMPA receptor auxiliary protein 3) Predicted to enable channel regulator activity. Involved in regulation of AMPA receptor activity. Predicted to be located in dendritic shaft and postsynaptic membrane. Predicted to be part of AMPA glutamate receptor complex. Predicted to be active in dendrite and glutamatergic synapse. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNIH3	NM_152495.2	c.82-2870C>G		intron_variant	Intron 1 of 5	ENST00000272133.4	NP_689708.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNIH3	ENST00000272133.4	c.82-2870C>G		intron_variant	Intron 1 of 5	1	NM_152495.2	ENSP00000272133.3

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29580 AN: 151876 Hom.: 3206 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.0846

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.195 AC: 29614 AN: 151994 Hom.: 3212 Cov.: 32 AF XY: 0.195 AC XY: 14464 AN XY: 74268

African (AFR) AF: 0.295 AC: 12219 AN: 41420

American (AMR) AF: 0.119 AC: 1817 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 607 AN: 3468

East Asian (EAS) AF: 0.116 AC: 599 AN: 5178

South Asian (SAS) AF: 0.111 AC: 533 AN: 4808

European-Finnish (FIN) AF: 0.204 AC: 2143 AN: 10526

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11195 AN: 67990

Other (OTH) AF: 0.182 AC: 385 AN: 2110

Alfa AF: 0.184 Hom.: 334

Bravo AF: 0.194

Asia WGS AF: 0.119 AC: 413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.65
PhyloP100		0.026
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: rs930323; hg19: chr1-224865790;