rs10865016

Variant names:

• chr2-98372841-G-A
• rs10865016
• NM_001298.3:c.101+2765G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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]

CNGA3 Gene-Disease associations (from GenCC):

• achromatopsia 2

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Illumina, G2P, Labcorp Genetics (formerly Invitae)
• CNGA3-related retinopathy

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• cone-rod dystrophy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• achromatopsia

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

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 = 0.34 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001298.3. 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
	CNGA3	NM_001298.3	MANE Select	c.101+2765G>A		intron	N/A	NP_001289.1	Q16281-1
	CNGA3	NM_001079878.2		c.101+2765G>A		intron	N/A	NP_001073347.1	Q16281-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNGA3	ENST00000272602.7	TSL:1 MANE Select	c.101+2765G>A		intron	N/A	ENSP00000272602.2	Q16281-1
	CNGA3	ENST00000436404.6	TSL:1	c.101+2765G>A		intron	N/A	ENSP00000410070.2	Q16281-2
	CNGA3	ENST00000853268.1		c.101+2765G>A		intron	N/A	ENSP00000523327.1

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

African (AFR) AF: 0.184 AC: 7641 AN: 41444

American (AMR) AF: 0.348 AC: 5304 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1117 AN: 3470

East Asian (EAS) AF: 0.349 AC: 1799 AN: 5148

South Asian (SAS) AF: 0.173 AC: 832 AN: 4802

European-Finnish (FIN) AF: 0.165 AC: 1739 AN: 10546

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13128 AN: 67948

Other (OTH) AF: 0.241 AC: 505 AN: 2098

Alfa AF: 0.116 Hom.: 217

Bravo AF: 0.233

Asia WGS AF: 0.263 AC: 916 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	10
DANN	Benign	0.75
PhyloP100		1.4
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: rs10865016; hg19: chr2-98989304;