22-36723755-C-T

Variant summary

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

The NR_134623.1(CACNG2-DT):n.237+408C>T 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 0.641 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 NR_134623.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.336

Genes affected

CACNG2-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CACNG2-DT	NR_134623.1	n.237+408C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.694

Gnomad4 ASJ AF: 0.722

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.700

Gnomad4 NFE AF: 0.732

Gnomad4 OTH AF: 0.678

Alfa AF: 0.718 Hom.: 49586

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs738518; hg19: chr22-37119800;