rs4961216

Variant names:

• chr8-86748779-A-C
• rs4961216
• ENST00000519041.1:n.449-12057A>C

Variant summary

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

The ENST00000519041.1(CNGB3-AS1):​n.449-12057A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,190 control chromosomes in the GnomAD database, including 993 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 0.10 (993 hom., cov: 33)
• Consequence: CNGB3-AS1 ENST00000519041.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.05
• Publications: 2 publications found

Genes affected

CNGB3-AS1 (HGNC:58258):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000519041.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNGB3-AS1	ENST00000519041.1	TSL:3	n.449-12057A>C		intron	N/A
	CNGB3-AS1	ENST00000805695.1		n.380-23517A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15308 AN: 152070 Hom.: 990 Cov.: 33

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0815

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.0444

Gnomad FIN AF: 0.0623

Gnomad MID AF: 0.122

Gnomad NFE AF: 0.0586

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.101 AC: 15348 AN: 152190 Hom.: 993 Cov.: 33 AF XY: 0.101 AC XY: 7532 AN XY: 74398

African (AFR) AF: 0.179 AC: 7443 AN: 41510

American (AMR) AF: 0.113 AC: 1726 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0815 AC: 283 AN: 3472

East Asian (EAS) AF: 0.133 AC: 688 AN: 5192

South Asian (SAS) AF: 0.0442 AC: 213 AN: 4820

European-Finnish (FIN) AF: 0.0623 AC: 661 AN: 10608

Middle Eastern (MID) AF: 0.131 AC: 38 AN: 290

European-Non Finnish (NFE) AF: 0.0586 AC: 3985 AN: 67974

Other (OTH) AF: 0.113 AC: 240 AN: 2116

Alfa AF: 0.0683 Hom.: 580

Bravo AF: 0.108

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	13
DANN	Benign	0.69
PhyloP100		2.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4961216;

hg19: chr8-87761007;