rs6085569

Variant names:

• chr20-6472458-C-G
• rs6085569
• ENST00000415932.1:n.102-1081C>G

Your query was ambiguous. Multiple possible variants found:

• chr20-6472458-C-G
• chr20-6472458-C-T

Variant summary

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

The ENST00000415932.1(CASC20):​n.102-1081C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,142 control chromosomes in the GnomAD database, including 2,936 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 (2936 hom., cov: 33)
• Consequence: CASC20 ENST00000415932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CASC20	NR_109953.1	n.181-1081C>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CASC20	ENST00000415932.1	n.102-1081C>G		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28414 AN: 152024 Hom.: 2934 Cov.: 33

Gnomad AFR AF: 0.0938

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.187 AC: 28415 AN: 152142 Hom.: 2936 Cov.: 33 AF XY: 0.188 AC XY: 14000 AN XY: 74354

African (AFR) AF: 0.0936 AC: 3889 AN: 41530

American (AMR) AF: 0.192 AC: 2932 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 699 AN: 3472

East Asian (EAS) AF: 0.139 AC: 720 AN: 5182

South Asian (SAS) AF: 0.183 AC: 884 AN: 4822

European-Finnish (FIN) AF: 0.272 AC: 2877 AN: 10562

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15799 AN: 67980

Other (OTH) AF: 0.168 AC: 354 AN: 2110

Alfa AF: 0.0961 Hom.: 199

Bravo AF: 0.177

Asia WGS AF: 0.145 AC: 507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.95
DANN	Benign	0.71
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs6085569; hg19: chr20-6453105;