rs10799590

Variant names:

• chr1-224634780-G-A
• rs10799590
• NM_152495.2:c.81+17525G>A

Variant summary

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

The NM_152495.2(CNIH3):​c.81+17525G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151,760 control chromosomes in the GnomAD database, including 25,334 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 0.56 (25334 hom., cov: 30)
• Consequence: CNIH3 NM_152495.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.457
• Publications: 17 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152495.2. 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
	CNIH3	NM_152495.2	MANE Select	c.81+17525G>A		intron	N/A	NP_689708.1	Q8TBE1
	CNIH3	NM_001322302.2		c.166-46178G>A		intron	N/A	NP_001309231.1
	CNIH3	NM_001322303.2		c.100-46178G>A		intron	N/A	NP_001309232.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNIH3	ENST00000272133.4	TSL:1 MANE Select	c.81+17525G>A		intron	N/A	ENSP00000272133.3	Q8TBE1
	CNIH3	ENST00000860910.1		c.81+17525G>A		intron	N/A	ENSP00000530969.1
	CNIH3	ENST00000933029.1		c.81+17525G>A		intron	N/A	ENSP00000603088.1

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84836 AN: 151640 Hom.: 25293 Cov.: 30

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.560 AC: 84935 AN: 151760 Hom.: 25334 Cov.: 30 AF XY: 0.567 AC XY: 42020 AN XY: 74140

African (AFR) AF: 0.755 AC: 31190 AN: 41332

American (AMR) AF: 0.587 AC: 8959 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1273 AN: 3464

East Asian (EAS) AF: 0.779 AC: 4013 AN: 5150

South Asian (SAS) AF: 0.529 AC: 2537 AN: 4796

European-Finnish (FIN) AF: 0.539 AC: 5669 AN: 10520

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29669 AN: 67906

Other (OTH) AF: 0.516 AC: 1089 AN: 2112

Alfa AF: 0.471 Hom.: 76329

Bravo AF: 0.576

Asia WGS AF: 0.626 AC: 2178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.41
DANN	Benign	0.56
PhyloP100		-0.46
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: rs10799590; hg19: chr1-224822482;