1-224677050-A-T

Position:

• chr1-224677050-A-T

Variant summary

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

The NM_152495.2(CNIH3):​c.82-3908A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 152,088 control chromosomes in the GnomAD database, including 15,116 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 0.41 (15116 hom., cov: 32)
• Consequence: CNIH3 NM_152495.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.538

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=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNIH3	NM_152495.2	c.82-3908A>T		intron_variant		ENST00000272133.4	NP_689708.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNIH3	ENST00000272133.4	c.82-3908A>T		intron_variant		1	NM_152495.2	ENSP00000272133.3

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62555 AN: 151970 Hom.: 15117 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.411 AC: 62556 AN: 152088 Hom.: 15116 Cov.: 32 AF XY: 0.405 AC XY: 30095 AN XY: 74350

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.640

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.554

Gnomad4 OTH AF: 0.459

Alfa AF: 0.478 Hom.: 2345

Bravo AF: 0.393

Asia WGS AF: 0.381 AC: 1325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.1
DANN	Benign	0.92

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: rs1369847; hg19: chr1-224864752;