rs1883988

Variant names:

• chr22-36709135-G-A
• rs1883988
• ENST00000732673.1:n.254G>A

Variant summary

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

The ENST00000732673.1(CACNG2-DT):​n.254G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,060 control chromosomes in the GnomAD database, including 4,899 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 0.25 (4899 hom., cov: 32)
• Consequence: CACNG2-DT ENST00000732673.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 8 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNG2-DT	NR_134623.1	n.117+5143G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNG2-DT	ENST00000732673.1	n.254G>A		non_coding_transcript_exon_variant	Exon 2 of 3
CACNG2-DT	ENST00000430281.4	n.416+5143G>A		intron_variant	Intron 1 of 1	2
CACNG2-DT	ENST00000732668.1	n.312+5143G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37896 AN: 151942 Hom.: 4905 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.249 AC: 37894 AN: 152060 Hom.: 4899 Cov.: 32 AF XY: 0.252 AC XY: 18695 AN XY: 74308

African (AFR) AF: 0.177 AC: 7363 AN: 41486

American (AMR) AF: 0.246 AC: 3765 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 821 AN: 3470

East Asian (EAS) AF: 0.305 AC: 1576 AN: 5164

South Asian (SAS) AF: 0.307 AC: 1474 AN: 4800

European-Finnish (FIN) AF: 0.344 AC: 3632 AN: 10570

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18411 AN: 67970

Other (OTH) AF: 0.249 AC: 525 AN: 2112

Alfa AF: 0.257 Hom.: 16377

Bravo AF: 0.236

Asia WGS AF: 0.265 AC: 919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.22
DANN	Benign	0.58
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1883988; hg19: chr22-37105180;