rs2423161

Variant names:

• chr20-6529233-A-C
• rs2423161
• ENST00000722184.1:n.297-39397A>C

Variant summary

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

The ENST00000722184.1(CASC20):​n.297-39397A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,172 control chromosomes in the GnomAD database, including 2,449 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 0.16 (2449 hom., cov: 32)
• Consequence: CASC20 ENST00000722184.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.56
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.274 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC20	ENST00000722184.1		n.297-39397A>C		intron	N/A
	CASC20	ENST00000722185.1		n.280-39397A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23655 AN: 152054 Hom.: 2431 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.00750

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0431

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.156 AC: 23713 AN: 152172 Hom.: 2449 Cov.: 32 AF XY: 0.151 AC XY: 11215 AN XY: 74422

African (AFR) AF: 0.278 AC: 11533 AN: 41466

American (AMR) AF: 0.120 AC: 1828 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 883 AN: 3468

East Asian (EAS) AF: 0.00732 AC: 38 AN: 5190

South Asian (SAS) AF: 0.115 AC: 557 AN: 4824

European-Finnish (FIN) AF: 0.0431 AC: 457 AN: 10614

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

European-Non Finnish (NFE) AF: 0.117 AC: 7925 AN: 68012

Other (OTH) AF: 0.176 AC: 373 AN: 2114

Alfa AF: 0.130 Hom.: 883

Bravo AF: 0.165

Asia WGS AF: 0.0890 AC: 312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.2
DANN	Benign	0.65
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs2423161; hg19: chr20-6509880;