4-47942012-CAAAAAA-CAAAAA

Variant names:

• chr4-47942012-CA-C
• rs10709670
• NM_001379270.1:c.545+28delT

Variant summary

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

The NM_001379270.1(CNGA1):​c.545+28delT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.78 (37387 hom., cov: 0)
  • Exomes 𝑓: 0.44 (3181 hom.)
  • Failed GnomAD Quality Control
• Consequence: CNGA1 NM_001379270.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.500

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:27194): (NIPA like domain containing 1) Predicted to enable magnesium ion transmembrane transporter activity. Predicted to be involved in magnesium ion transport. Predicted to be integral component of membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]

LOC101927157 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 4-47942012-CA-C is Benign according to our data. Variant chr4-47942012-CA-C is described in ClinVar as [Benign]. Clinvar id is 1235728.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr4-47942012-CA-C is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNGA1	NM_001379270.1	c.545+28delT		intron_variant	Intron 9 of 10	ENST00000514170.7	NP_001366199.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNGA1	ENST00000514170.7	c.545+28delT		intron_variant	Intron 9 of 10	5	NM_001379270.1	ENSP00000426862.3

Frequencies

GnomAD3 genomes AF: 0.776 AC: 99136 AN: 127692 Hom.: 37397 Cov.: 0

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.754

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.443 AC: 457010 AN: 1031280 Hom.: 3181 Cov.: 0 AF XY: 0.443 AC XY: 232304 AN XY: 524808

Gnomad4 AFR exome AF: 0.463

Gnomad4 AMR exome AF: 0.450

Gnomad4 ASJ exome AF: 0.408

Gnomad4 EAS exome AF: 0.482

Gnomad4 SAS exome AF: 0.435

Gnomad4 FIN exome AF: 0.444

Gnomad4 NFE exome AF: 0.442

Gnomad4 OTH exome AF: 0.447

GnomAD4 genome AF: 0.776 AC: 99132 AN: 127702 Hom.: 37387 Cov.: 0 AF XY: 0.778 AC XY: 47715 AN XY: 61308

Gnomad4 AFR AF: 0.835

Gnomad4 AMR AF: 0.810

Gnomad4 ASJ AF: 0.662

Gnomad4 EAS AF: 0.954

Gnomad4 SAS AF: 0.736

Gnomad4 FIN AF: 0.773

Gnomad4 NFE AF: 0.732

Gnomad4 OTH AF: 0.755

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

May 10, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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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;