ENST00000533426.5:c.-58-537A>T

Variant names:

• chr11-6238847-A-T
• rs325703
• ENST00000533426.5:c.-58-537A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000533426.5(CNGA4):​c.-58-537A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0223 in 152,302 control chromosomes in the GnomAD database, including 117 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 0.022 (117 hom., cov: 32)
• Consequence: CNGA4 ENST00000533426.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.538
• Publications: 1 publications found

Genes affected

CNGA4 (HGNC:2152): (cyclic nucleotide gated channel subunit alpha 4) CNGA4 is a modulatory subunit of vertebrate cyclic nucleotide-gated membrane channels that transduce odorant signals (Munger et al., 2001 [PubMed 11739959]).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0714 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000533426.5. 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
	CNGA4	NM_001037329.4	MANE Select	c.-360A>T		upstream_gene	N/A	NP_001032406.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNGA4	ENST00000533426.5	TSL:2	c.-58-537A>T		intron	N/A	ENSP00000433399.1
	CNGA4	ENST00000379936.3	TSL:1 MANE Select	c.-360A>T		upstream_gene	N/A	ENSP00000369268.2
	CNGA4	ENST00000872205.1		c.-360A>T		upstream_gene	N/A	ENSP00000542264.1

Frequencies

GnomAD3 genomes AF: 0.0222 AC: 3385 AN: 152184 Hom.: 115 Cov.: 32

Gnomad AFR AF: 0.0736

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0137

Gnomad ASJ AF: 0.00807

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00186

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.000676

Gnomad OTH AF: 0.0182

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

GnomAD4 genome AF: 0.0223 AC: 3395 AN: 152302 Hom.: 117 Cov.: 32 AF XY: 0.0217 AC XY: 1613 AN XY: 74474

African (AFR) AF: 0.0736 AC: 3058 AN: 41538

American (AMR) AF: 0.0137 AC: 210 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00807 AC: 28 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5186

South Asian (SAS) AF: 0.00166 AC: 8 AN: 4828

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10624

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.000676 AC: 46 AN: 68036

Other (OTH) AF: 0.0180 AC: 38 AN: 2108

Alfa AF: 0.0170 Hom.: 7

Bravo AF: 0.0262

Asia WGS AF: 0.00779 AC: 28 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.0
DANN	Benign	0.79
PhyloP100		-0.54
PromoterAI		0.032	Neutral
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs325703; hg19: chr11-6260077;