rs13418293

Positions:

• chr2-98354428-C-A
• chr2-98354428-C-G
• chr2-98354428-C-T

Variant summary

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

The ENST00000272602.7(CNGA3):​c.-38+7894C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 151,910 control chromosomes in the GnomAD database, including 3,592 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 (3592 hom., cov: 32)
• Consequence: CNGA3 ENST00000272602.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.685

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNGA3	NM_001298.3	c.-38+7894C>A		intron_variant		ENST00000272602.7	NP_001289.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNGA3	ENST00000272602.7	c.-38+7894C>A		intron_variant		1	NM_001298.3	ENSP00000272602	A1
CNGA3	ENST00000436404.6	c.-38+7894C>A		intron_variant		1		ENSP00000410070	P4
	ENST00000454230.1	n.191+1387G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31224 AN: 151792 Hom.: 3588 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.00618

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.206 AC: 31253 AN: 151910 Hom.: 3592 Cov.: 32 AF XY: 0.198 AC XY: 14687 AN XY: 74246

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.00619

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.226

Alfa AF: 0.128 Hom.: 236

Bravo AF: 0.207

Asia WGS AF: 0.0710 AC: 249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.8
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: rs13418293; hg19: chr2-98970891;