chr4-48005105-ATTAT-A

Variant names:

• chr4-48005105-ATTAT-A
• rs58158986
• NM_001379270.1:c.-123+5685_-123+5688delATAA

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001379270.1(CNGA1):​c.-123+5685_-123+5688delATAA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.00065 (0 hom., cov: 0)
• Consequence: CNGA1 NM_001379270.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121

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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNGA1	NM_001379270.1	c.-123+5685_-123+5688delATAA		intron_variant	Intron 2 of 10	ENST00000514170.7	NP_001366199.1
CNGA1	NM_000087.5	c.-123+5685_-123+5688delATAA		intron_variant	Intron 2 of 10		NP_000078.3
CNGA1	XM_005248049.5	c.-3+11374_-3+11377delATAA		intron_variant	Intron 1 of 8		XP_005248106.3
CNGA1	XM_011513623.3	c.-3+5685_-3+5688delATAA		intron_variant	Intron 2 of 9		XP_011511925.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNGA1	ENST00000514170.7	c.-123+5685_-123+5688delATAA		intron_variant	Intron 2 of 10	5	NM_001379270.1	ENSP00000426862.3

Frequencies

GnomAD3 genomes AF: 0.000647 AC: 94 AN: 145372 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000943

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000548

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00318

Gnomad SAS AF: 0.00268

Gnomad FIN AF: 0.000212

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000257

Gnomad OTH AF: 0.00102

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

GnomAD4 genome AF: 0.000653 AC: 95 AN: 145486 Hom.: 0 Cov.: 0 AF XY: 0.000693 AC XY: 49 AN XY: 70756

African (AFR) AF: 0.000966 AC: 38 AN: 39344

American (AMR) AF: 0.000548 AC: 8 AN: 14610

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3352

East Asian (EAS) AF: 0.00319 AC: 16 AN: 5014

South Asian (SAS) AF: 0.00268 AC: 12 AN: 4472

European-Finnish (FIN) AF: 0.000212 AC: 2 AN: 9450

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 284

European-Non Finnish (NFE) AF: 0.000257 AC: 17 AN: 66084

Other (OTH) AF: 0.00101 AC: 2 AN: 1982

Alfa AF: 0.000161 Hom.: 960

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.12

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: rs58158986; hg19: chr4-48007122;