1-224692009-A-G

Position:

• chr1-224692009-A-G

Variant summary

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

The NM_152495.2(CNIH3):​c.198+7166A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0424 in 152,318 control chromosomes in the GnomAD database, including 218 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 0.042 (218 hom., cov: 33)
• Consequence: CNIH3 NM_152495.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

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]

CNIH3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNIH3	NM_152495.2	c.198+7166A>G		intron_variant		ENST00000272133.4	NP_689708.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNIH3	ENST00000272133.4	c.198+7166A>G		intron_variant		1	NM_152495.2	ENSP00000272133.3
CNIH3	ENST00000478120.5	n.519+7166A>G		intron_variant		5
CNIH3	ENST00000481095.5	n.490+7166A>G		intron_variant		3
CNIH3	ENST00000498382.5	n.347+7166A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0424 AC: 6450 AN: 152200 Hom.: 216 Cov.: 33

Gnomad AFR AF: 0.0186

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0759

Gnomad ASJ AF: 0.0205

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.0800

Gnomad FIN AF: 0.0258

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0413

Gnomad OTH AF: 0.0526

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

GnomAD4 genome AF: 0.0424 AC: 6455 AN: 152318 Hom.: 218 Cov.: 33 AF XY: 0.0439 AC XY: 3266 AN XY: 74474

Gnomad4 AFR AF: 0.0185

Gnomad4 AMR AF: 0.0761

Gnomad4 ASJ AF: 0.0205

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.0803

Gnomad4 FIN AF: 0.0258

Gnomad4 NFE AF: 0.0413

Gnomad4 OTH AF: 0.0526

Alfa AF: 0.0133 Hom.: 5

Bravo AF: 0.0464

Asia WGS AF: 0.117 AC: 408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.42
DANN	Benign	0.47

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: rs10495226; hg19: chr1-224879711;