rs10865016

Positions:

• chr2-98372841-G-A
• chr2-98372841-G-C
• chr2-98372841-G-T

Variant summary

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

The NM_001298.3(CNGA3):​c.101+2765G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 151,916 control chromosomes in the GnomAD database, including 3,760 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 0.21 (3760 hom., cov: 32)
• Consequence: CNGA3 NM_001298.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39

Genes affected

CNGA3 (HGNC:2150): (cyclic nucleotide gated channel subunit alpha 3) This gene encodes a member of the cyclic nucleotide-gated cation channel protein family which is required for normal vision and olfactory signal transduction. Mutations in this gene are associated with achromatopsia (rod monochromacy) and color blindness. Two alternatively spliced transcripts encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

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 = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNGA3	NM_001298.3	c.101+2765G>A		intron_variant		ENST00000272602.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNGA3	ENST00000272602.7	c.101+2765G>A		intron_variant		1	NM_001298.3	A1
CNGA3	ENST00000436404.6	c.101+2765G>A		intron_variant		1		P4

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32362 AN: 151798 Hom.: 3749 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.213 AC: 32393 AN: 151916 Hom.: 3760 Cov.: 32 AF XY: 0.215 AC XY: 15988 AN XY: 74248

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.241

Alfa AF: 0.113 Hom.: 199

Bravo AF: 0.233

Asia WGS AF: 0.263 AC: 916 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	10
DANN	Benign	0.75

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: rs10865016; hg19: chr2-98989304;