20-6487614-G-T

Variant names:

• chr20-6487614-G-T
• rs10485705
• ENST00000415932.1:n.218+13959G>T

Variant summary

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

The NR_109953.1(CASC20):​n.297+13959G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,140 control chromosomes in the GnomAD database, including 3,908 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 0.20 (3908 hom., cov: 32)
• Consequence: CASC20 NR_109953.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_109953.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC20	NR_109953.1		n.297+13959G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC20	ENST00000415932.1	TSL:5	n.218+13959G>T		intron	N/A
	CASC20	ENST00000722184.1		n.296+13959G>T		intron	N/A
	CASC20	ENST00000722185.1		n.279+3389G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30680 AN: 152022 Hom.: 3906 Cov.: 32

Gnomad AFR AF: 0.0501

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.202 AC: 30676 AN: 152140 Hom.: 3908 Cov.: 32 AF XY: 0.200 AC XY: 14910 AN XY: 74372

African (AFR) AF: 0.0499 AC: 2072 AN: 41538

American (AMR) AF: 0.235 AC: 3590 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 862 AN: 3468

East Asian (EAS) AF: 0.117 AC: 606 AN: 5182

South Asian (SAS) AF: 0.195 AC: 941 AN: 4814

European-Finnish (FIN) AF: 0.272 AC: 2880 AN: 10578

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18977 AN: 67960

Other (OTH) AF: 0.200 AC: 423 AN: 2112

Alfa AF: 0.260 Hom.: 6857

Bravo AF: 0.192

Asia WGS AF: 0.134 AC: 466 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	1.7
DANN	Benign	0.32
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs10485705; hg19: chr20-6468261;