16-57882799-CTTTTTTTT-CTTTTTTTTT

Variant names:

• chr16-57882799-C-CT
• rs71155213
• NM_001297.5:c.*1364dupA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001297.5(CNGB1):​c.*1364dupA variant causes a 3 prime UTR 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 0.031 (101 hom., cov: 18)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CNGB1 NM_001297.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 0 publications found

Genes affected

CNGB1 (HGNC:2151): (cyclic nucleotide gated channel subunit beta 1) In humans, the rod photoreceptor cGMP-gated cation channel helps regulate ion flow into the rod photoreceptor outer segment in response to light-induced alteration of the levels of intracellular cGMP. This channel consists of two subunits, alpha and beta, with the protein encoded by this gene representing the beta subunit. Defects in this gene are a cause of cause of retinitis pigmentosa type 45. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2013]

CNGB1 Gene-Disease associations (from GenCC):

• CNGB1-related retinopathy

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• retinitis pigmentosa 45

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
• retinitis pigmentosa

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0678 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001297.5. 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
	CNGB1	NM_001297.5	MANE Select	c.*1364dupA		3_prime_UTR	Exon 33 of 33	NP_001288.3	Q14028-1
	CNGB1	NM_001286130.2		c.*1364dupA		3_prime_UTR	Exon 33 of 33	NP_001273059.1	Q14028-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNGB1	ENST00000251102.13	TSL:1 MANE Select	c.*1364dupA		3_prime_UTR	Exon 33 of 33	ENSP00000251102.8	Q14028-1

Frequencies

GnomAD3 genomes AF: 0.0307 AC: 4181 AN: 135998 Hom.: 101 Cov.: 18

Gnomad AFR AF: 0.0701

Gnomad AMI AF: 0.00353

Gnomad AMR AF: 0.0190

Gnomad ASJ AF: 0.0226

Gnomad EAS AF: 0.00272

Gnomad SAS AF: 0.0181

Gnomad FIN AF: 0.0113

Gnomad MID AF: 0.0548

Gnomad NFE AF: 0.0162

Gnomad OTH AF: 0.0341

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0308 AC: 4184 AN: 136016 Hom.: 101 Cov.: 18 AF XY: 0.0306 AC XY: 2008 AN XY: 65564

African (AFR) AF: 0.0701 AC: 2576 AN: 36770

American (AMR) AF: 0.0190 AC: 256 AN: 13508

Ashkenazi Jewish (ASJ) AF: 0.0226 AC: 73 AN: 3228

East Asian (EAS) AF: 0.00273 AC: 13 AN: 4766

South Asian (SAS) AF: 0.0182 AC: 78 AN: 4288

European-Finnish (FIN) AF: 0.0113 AC: 85 AN: 7514

Middle Eastern (MID) AF: 0.0602 AC: 16 AN: 266

European-Non Finnish (NFE) AF: 0.0162 AC: 1019 AN: 62908

Other (OTH) AF: 0.0339 AC: 65 AN: 1918

Alfa AF: 0.00443 Hom.: 199

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.0

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

Other links and lift over

dbSNP: rs71155213; hg19: chr16-57916703;