rs6038520

Variant names:

• chr20-6482970-C-T
• rs6038520
• ENST00000415932.1:n.218+9315C>T

Variant summary

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

The ENST00000415932.1(CASC20):​n.218+9315C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 151,110 control chromosomes in the GnomAD database, including 6,441 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 0.28 (6441 hom., cov: 31)
• Consequence: CASC20 ENST00000415932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.838
• Publications: 5 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 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+9315C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC20	ENST00000415932.1	TSL:5	n.218+9315C>T		intron	N/A
	CASC20	ENST00000722184.1		n.296+9315C>T		intron	N/A
	CASC20	ENST00000722185.1		n.182-1158C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.285 AC: 42983 AN: 150994 Hom.: 6421 Cov.: 31

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.285 AC: 43036 AN: 151110 Hom.: 6441 Cov.: 31 AF XY: 0.288 AC XY: 21221 AN XY: 73768

African (AFR) AF: 0.386 AC: 15898 AN: 41234

American (AMR) AF: 0.232 AC: 3517 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 777 AN: 3460

East Asian (EAS) AF: 0.261 AC: 1343 AN: 5144

South Asian (SAS) AF: 0.318 AC: 1527 AN: 4806

European-Finnish (FIN) AF: 0.319 AC: 3250 AN: 10198

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15949 AN: 67780

Other (OTH) AF: 0.246 AC: 517 AN: 2098

Alfa AF: 0.259 Hom.: 1874

Bravo AF: 0.281

Asia WGS AF: 0.267 AC: 929 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.49
DANN	Benign	0.25
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs6038520; hg19: chr20-6463617;