rs5750285

Variant names:

• chr22-36708203-C-G
• rs5750285
• ENST00000430281.4:n.416+4211C>G

Variant summary

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

The ENST00000430281.4(CACNG2-DT):​n.416+4211C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 151,830 control chromosomes in the GnomAD database, including 20,445 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 0.51 (20445 hom., cov: 31)
• Consequence: CACNG2-DT ENST00000430281.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127
• Publications: 6 publications found

Genes affected

CACNG2-DT (HGNC:55682): (CACNG2 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000430281.4. 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
	CACNG2-DT	NR_134623.1		n.117+4211C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CACNG2-DT	ENST00000430281.4	TSL:2	n.416+4211C>G		intron	N/A
	CACNG2-DT	ENST00000732668.1		n.312+4211C>G		intron	N/A
	CACNG2-DT	ENST00000732669.1		n.206+4211C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76726 AN: 151712 Hom.: 20413 Cov.: 31

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.506 AC: 76803 AN: 151830 Hom.: 20445 Cov.: 31 AF XY: 0.509 AC XY: 37779 AN XY: 74196

African (AFR) AF: 0.675 AC: 27913 AN: 41374

American (AMR) AF: 0.521 AC: 7942 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1114 AN: 3468

East Asian (EAS) AF: 0.462 AC: 2377 AN: 5150

South Asian (SAS) AF: 0.488 AC: 2349 AN: 4810

European-Finnish (FIN) AF: 0.549 AC: 5791 AN: 10552

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 27957 AN: 67902

Other (OTH) AF: 0.448 AC: 947 AN: 2114

Alfa AF: 0.480 Hom.: 2254

Bravo AF: 0.508

Asia WGS AF: 0.458 AC: 1591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.2
DANN	Benign	0.71
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs5750285; hg19: chr22-37104248;