20-6468031-T-G

Variant names:

• chr20-6468031-T-G
• rs6117277
• ENST00000415932.1:n.102-5508T>G

Variant summary

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

The ENST00000415932.1(CASC20):​n.102-5508T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.804 in 152,100 control chromosomes in the GnomAD database, including 49,327 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 0.80 (49327 hom., cov: 33)
• Consequence: CASC20 ENST00000415932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.867 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.181-5508T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC20	ENST00000415932.1	TSL:5	n.102-5508T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.804 AC: 122179 AN: 151982 Hom.: 49280 Cov.: 33

Gnomad AFR AF: 0.874

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.862

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.804 AC: 122281 AN: 152100 Hom.: 49327 Cov.: 33 AF XY: 0.803 AC XY: 59681 AN XY: 74336

African (AFR) AF: 0.874 AC: 36276 AN: 41492

American (AMR) AF: 0.805 AC: 12291 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.799 AC: 2771 AN: 3470

East Asian (EAS) AF: 0.862 AC: 4449 AN: 5164

South Asian (SAS) AF: 0.816 AC: 3936 AN: 4824

European-Finnish (FIN) AF: 0.727 AC: 7694 AN: 10580

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.768 AC: 52184 AN: 67978

Other (OTH) AF: 0.824 AC: 1738 AN: 2110

Alfa AF: 0.780 Hom.: 81702

Bravo AF: 0.813

Asia WGS AF: 0.852 AC: 2963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.44
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs6117277; hg19: chr20-6448678;