rs10799590

Positions:

• chr1-224634780-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNIH3	NM_152495.2	c.81+17525G>A		intron_variant		ENST00000272133.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNIH3	ENST00000272133.4	c.81+17525G>A		intron_variant		1	NM_152495.2	P1

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

Gnomad4 AFR AF: 0.755

Gnomad4 AMR AF: 0.587

Gnomad4 ASJ AF: 0.367

Gnomad4 EAS AF: 0.779

Gnomad4 SAS AF: 0.529

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.516

Alfa AF: 0.452 Hom.: 33314

Bravo AF: 0.576

Asia WGS AF: 0.626 AC: 2178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.41
DANN	Benign	0.56

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: rs10799590; hg19: chr1-224822482;