ENST00000415932.1:n.218+9210A>G

Variant names:

• chr20-6482865-A-G
• rs6054303
• ENST00000415932.1:n.218+9210A>G

Variant summary

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

The ENST00000415932.1(CASC20):​n.218+9210A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 151,948 control chromosomes in the GnomAD database, including 6,538 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 0.29 (6538 hom., cov: 32)
• Consequence: CASC20 ENST00000415932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.753
• Publications: 4 publications found

Genes affected

CASC20 (HGNC:49477): (cancer susceptibility 20)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000415932.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC20	NR_109953.1		n.297+9210A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC20	ENST00000415932.1	TSL:5	n.218+9210A>G		intron	N/A
	CASC20	ENST00000722184.1		n.296+9210A>G		intron	N/A
	CASC20	ENST00000722185.1		n.182-1263A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43411 AN: 151830 Hom.: 6519 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.286 AC: 43464 AN: 151948 Hom.: 6538 Cov.: 32 AF XY: 0.289 AC XY: 21444 AN XY: 74252

African (AFR) AF: 0.388 AC: 16062 AN: 41414

American (AMR) AF: 0.233 AC: 3557 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 779 AN: 3470

East Asian (EAS) AF: 0.261 AC: 1351 AN: 5174

South Asian (SAS) AF: 0.319 AC: 1533 AN: 4812

European-Finnish (FIN) AF: 0.321 AC: 3374 AN: 10526

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.236 AC: 16029 AN: 67962

Other (OTH) AF: 0.246 AC: 520 AN: 2112

Alfa AF: 0.182 Hom.: 511

Bravo AF: 0.282

Asia WGS AF: 0.268 AC: 934 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.7
DANN	Benign	0.78
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs6054303; hg19: chr20-6463512;