rs5750285

Positions:

• chr22-36708203-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_134623.1(CACNG2-DT):​n.117+4211C>G variant causes a intron, non coding transcript 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 NR_134623.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CACNG2-DT	NR_134623.1	n.117+4211C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CACNG2-DT	ENST00000430281.3	n.174+4211C>G		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.448

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5750285; hg19: chr22-37104248;