rs2180686

Variant names:

• chr20-6548823-T-C
• rs2180686
• ENST00000722184.1:n.297-19807T>C

Your query was ambiguous. Multiple possible variants found:

• chr20-6548823-T-C
• chr20-6548823-T-G

Variant summary

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

The ENST00000722184.1(CASC20):​n.297-19807T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.822 in 151,380 control chromosomes in the GnomAD database, including 51,402 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 0.82 (51402 hom., cov: 30)
• Consequence: CASC20 ENST00000722184.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.34
• 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=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.886 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.297-19807T>C		intron	N/A
	CASC20	ENST00000722185.1		n.280-19807T>C		intron	N/A
	CASC20	ENST00000722186.1		n.477+14079T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.821 AC: 124241 AN: 151262 Hom.: 51337 Cov.: 30

Gnomad AFR AF: 0.881

Gnomad AMI AF: 0.817

Gnomad AMR AF: 0.887

Gnomad ASJ AF: 0.872

Gnomad EAS AF: 0.907

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.839

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

GnomAD4 genome AF: 0.822 AC: 124363 AN: 151380 Hom.: 51402 Cov.: 30 AF XY: 0.821 AC XY: 60682 AN XY: 73920

African (AFR) AF: 0.881 AC: 36511 AN: 41436

American (AMR) AF: 0.887 AC: 13466 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.872 AC: 3019 AN: 3462

East Asian (EAS) AF: 0.907 AC: 4653 AN: 5128

South Asian (SAS) AF: 0.768 AC: 3698 AN: 4818

European-Finnish (FIN) AF: 0.762 AC: 8018 AN: 10524

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52227 AN: 67524

Other (OTH) AF: 0.842 AC: 1769 AN: 2102

Alfa AF: 0.796 Hom.: 74717

Bravo AF: 0.834

Asia WGS AF: 0.845 AC: 2927 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.069
DANN	Benign	0.63
PhyloP100		-2.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2180686;

hg19: chr20-6529470;

COSMIC: COSV50253327;