chr20-6547561-A-G

Variant names:

• chr20-6547561-A-G
• rs1576448
• ENST00000722184.1:n.297-21069A>G

Variant summary

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

The ENST00000722184.1(CASC20):​n.297-21069A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 151,820 control chromosomes in the GnomAD database, including 1,288 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 0.12 (1288 hom., cov: 32)
• Consequence: CASC20 ENST00000722184.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.833
• Publications: 1 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722184.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC20	ENST00000722184.1		n.297-21069A>G		intron	N/A
	CASC20	ENST00000722185.1		n.280-21069A>G		intron	N/A
	CASC20	ENST00000722186.1		n.477+12817A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18503 AN: 151700 Hom.: 1283 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.00757

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0448

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.122 AC: 18516 AN: 151820 Hom.: 1288 Cov.: 32 AF XY: 0.117 AC XY: 8714 AN XY: 74208

African (AFR) AF: 0.154 AC: 6363 AN: 41422

American (AMR) AF: 0.106 AC: 1609 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 882 AN: 3460

East Asian (EAS) AF: 0.00740 AC: 38 AN: 5138

South Asian (SAS) AF: 0.112 AC: 541 AN: 4810

European-Finnish (FIN) AF: 0.0448 AC: 475 AN: 10604

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8181 AN: 67870

Other (OTH) AF: 0.148 AC: 311 AN: 2108

Alfa AF: 0.115 Hom.: 150

Bravo AF: 0.127

Asia WGS AF: 0.0790 AC: 275 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.41
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs1576448; hg19: chr20-6528208;