rs59800634

Positions:

• chr4-47942012-CAA-C
• chr4-47942012-C-CAA
• chr4-47942012-CA-C
• chr4-47942012-CAAA-C
• chr4-47942012-C-CA
• chr4-47942012-C-CAAA
• chr4-47942012-CAAAAA-C
• chr4-47942012-CAAAA-C
• chr4-47942012-CAAAAAA-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001379270.1(CNGA1):​c.545+27_545+28delTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0778 in 1,150,820 control chromosomes in the GnomAD database, including 133 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.037 (80 hom., cov: 0)
  • Exomes 𝑓: 0.083 (53 hom.)
• Consequence: CNGA1 NM_001379270.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.526

Genes affected

CNGA1 (HGNC:2148): (cyclic nucleotide gated channel subunit alpha 1) The protein encoded by this gene is involved in phototransduction. Along with another protein, the encoded protein forms a cGMP-gated cation channel in the plasma membrane, allowing depolarization of rod photoreceptors. This represents the last step in the phototransduction pathway. Defects in this gene are a cause of retinitis pigmentosa autosomal recessive (ARRP) disease. Multiple transcript variants have been found for this gene. [provided by RefSeq, Oct 2019]

NIPAL1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 4-47942012-CAA-C is Benign according to our data. Variant chr4-47942012-CAA-C is described in ClinVar as [Benign]. Clinvar id is 1226008.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.087 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNGA1	NM_001379270.1	c.545+27_545+28delTT		intron_variant		ENST00000514170.7	NP_001366199.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNGA1	ENST00000514170.7	c.545+27_545+28delTT		intron_variant		5	NM_001379270.1	ENSP00000426862.3

Frequencies

GnomAD3 genomes AF: 0.0367 AC: 4687 AN: 127614 Hom.: 80 Cov.: 0

Gnomad AFR AF: 0.0198

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0271

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.00426

Gnomad SAS AF: 0.0226

Gnomad FIN AF: 0.0600

Gnomad MID AF: 0.0455

Gnomad NFE AF: 0.0500

Gnomad OTH AF: 0.0411

GnomAD4 exome AF: 0.0830 AC: 84892 AN: 1023200 Hom.: 53 AF XY: 0.0815 AC XY: 42469 AN XY: 520794

Gnomad4 AFR exome AF: 0.0701

Gnomad4 AMR exome AF: 0.0859

Gnomad4 ASJ exome AF: 0.0523

Gnomad4 EAS exome AF: 0.0599

Gnomad4 SAS exome AF: 0.0539

Gnomad4 FIN exome AF: 0.0939

Gnomad4 NFE exome AF: 0.0875

Gnomad4 OTH exome AF: 0.0753

GnomAD4 genome AF: 0.0368 AC: 4691 AN: 127620 Hom.: 80 Cov.: 0 AF XY: 0.0353 AC XY: 2165 AN XY: 61248

Gnomad4 AFR AF: 0.0199

Gnomad4 AMR AF: 0.0271

Gnomad4 ASJ AF: 0.0199

Gnomad4 EAS AF: 0.00428

Gnomad4 SAS AF: 0.0225

Gnomad4 FIN AF: 0.0600

Gnomad4 NFE AF: 0.0500

Gnomad4 OTH AF: 0.0415

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs10709670; hg19: chr4-47944029;