rs251850

chr19-53991509-T-Cchr19-53991509-T-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_102308.2(CACNG6):n.49+312T>C 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 0.188 in 148,160 control chromosomes in the GnomAD database, including 2,740 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 0.19 (2740 hom., cov: 29)
• Consequence: CACNG6 NR_102308.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.89

Genes affected

CACNG6 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CACNG6	NR_102308.2	n.49+312T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.188 AC: 27814 AN: 148038 Hom.: 2742 Cov.: 29

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.188 AC: 27806 AN: 148160 Hom.: 2740 Cov.: 29 AF XY: 0.185 AC XY: 13361 AN XY: 72198

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.181

Alfa AF: 0.217 Hom.: 4016

Bravo AF: 0.184

Asia WGS AF: 0.173 AC: 603 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
Cadd	Benign	20
Dann	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs251850; hg19: chr19-54494763;