rs3769755

chr2-98372955-C-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+2879C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.033 in 152,258 control chromosomes in the GnomAD database, including 403 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 0.033 (403 hom., cov: 32)
• Consequence: CNGA3 NM_001298.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNGA3	NM_001298.3	c.101+2879C>T		intron_variant		ENST00000272602.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNGA3	ENST00000272602.7	c.101+2879C>T		intron_variant		1	NM_001298.3	A1
CNGA3	ENST00000436404.6	c.101+2879C>T		intron_variant		1		P4

Frequencies

GnomAD3 genomes AF: 0.0329 AC: 5007 AN: 152140 Hom.: 400 Cov.: 32

Gnomad AFR AF: 0.0103

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.00519

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.0245

Gnomad FIN AF: 0.0163

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00848

Gnomad OTH AF: 0.0335

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

GnomAD4 genome AF: 0.0330 AC: 5025 AN: 152258 Hom.: 403 Cov.: 32 AF XY: 0.0366 AC XY: 2725 AN XY: 74446

Gnomad4 AFR AF: 0.0104

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.00519

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.0245

Gnomad4 FIN AF: 0.0163

Gnomad4 NFE AF: 0.00848

Gnomad4 OTH AF: 0.0327

Alfa AF: 0.0496 Hom.: 131

Bravo AF: 0.0499

Asia WGS AF: 0.0720 AC: 250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	6.3
Dann	Benign	0.85

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: rs3769755; hg19: chr2-98989418;