rs715541

Variant names:

• chr22-36720053-G-A
• rs715541
• ENST00000430281.4:n.417-863G>A

Variant summary

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

The ENST00000430281.4(CACNG2-DT):​n.417-863G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 151,956 control chromosomes in the GnomAD database, including 24,026 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 0.55 (24026 hom., cov: 30)
• Consequence: CACNG2-DT ENST00000430281.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.770
• Publications: 3 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNG2-DT	NR_134623.1	n.118-3175G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNG2-DT	ENST00000430281.4	n.417-863G>A		intron_variant	Intron 1 of 1	2
CACNG2-DT	ENST00000732668.1	n.313-3175G>A		intron_variant	Intron 1 of 2
CACNG2-DT	ENST00000732669.1	n.207-3175G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83584 AN: 151838 Hom.: 24016 Cov.: 30

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.550 AC: 83626 AN: 151956 Hom.: 24026 Cov.: 30 AF XY: 0.548 AC XY: 40719 AN XY: 74260

African (AFR) AF: 0.372 AC: 15404 AN: 41420

American (AMR) AF: 0.628 AC: 9587 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.653 AC: 2267 AN: 3470

East Asian (EAS) AF: 0.533 AC: 2753 AN: 5166

South Asian (SAS) AF: 0.555 AC: 2675 AN: 4818

European-Finnish (FIN) AF: 0.527 AC: 5556 AN: 10542

Middle Eastern (MID) AF: 0.664 AC: 194 AN: 292

European-Non Finnish (NFE) AF: 0.638 AC: 43350 AN: 67952

Other (OTH) AF: 0.590 AC: 1246 AN: 2112

Alfa AF: 0.615 Hom.: 113714

Bravo AF: 0.554

Asia WGS AF: 0.557 AC: 1942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.6
DANN	Benign	0.69
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs715541; hg19: chr22-37116098;