chr22-36723755-C-T

Variant names:

• chr22-36723755-C-T
• rs738518
• ENST00000732668.1:n.432+408C>T

Variant summary

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

The ENST00000732668.1(CACNG2-DT):​n.432+408C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 151,976 control chromosomes in the GnomAD database, including 32,264 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 0.64 (32264 hom., cov: 32)
• Consequence: CACNG2-DT ENST00000732668.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.336
• Publications: 9 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNG2-DT	NR_134623.1	n.237+408C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNG2-DT	ENST00000732668.1	n.432+408C>T		intron_variant	Intron 2 of 2
CACNG2-DT	ENST00000732669.1	n.326+408C>T		intron_variant	Intron 2 of 3
CACNG2-DT	ENST00000732670.1	n.279+408C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97349 AN: 151858 Hom.: 32242 Cov.: 32

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.722

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.742

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.641 AC: 97416 AN: 151976 Hom.: 32264 Cov.: 32 AF XY: 0.641 AC XY: 47623 AN XY: 74294

African (AFR) AF: 0.463 AC: 19156 AN: 41394

American (AMR) AF: 0.694 AC: 10602 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.722 AC: 2504 AN: 3466

East Asian (EAS) AF: 0.550 AC: 2841 AN: 5164

South Asian (SAS) AF: 0.587 AC: 2832 AN: 4822

European-Finnish (FIN) AF: 0.700 AC: 7404 AN: 10578

Middle Eastern (MID) AF: 0.760 AC: 222 AN: 292

European-Non Finnish (NFE) AF: 0.732 AC: 49773 AN: 67960

Other (OTH) AF: 0.678 AC: 1426 AN: 2102

Alfa AF: 0.709 Hom.: 62106

Bravo AF: 0.636

Asia WGS AF: 0.582 AC: 2029 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.47
DANN	Benign	0.61
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs738518; hg19: chr22-37119800;