chr20-6426995-G-A

Variant names:

• chr20-6426995-G-A
• rs6139980
• NR_109953.1:n.79+185G>A

Variant summary

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

The NR_109953.1(CASC20):​n.79+185G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 151,726 control chromosomes in the GnomAD database, including 13,007 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 0.41 (13007 hom., cov: 30)
• Consequence: CASC20 NR_109953.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.46 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.79+185G>A		intron	N/A

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62029 AN: 151608 Hom.: 12996 Cov.: 30

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.409 AC: 62071 AN: 151726 Hom.: 13007 Cov.: 30 AF XY: 0.406 AC XY: 30108 AN XY: 74128

African (AFR) AF: 0.295 AC: 12223 AN: 41368

American (AMR) AF: 0.414 AC: 6313 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1483 AN: 3462

East Asian (EAS) AF: 0.466 AC: 2398 AN: 5148

South Asian (SAS) AF: 0.403 AC: 1927 AN: 4778

European-Finnish (FIN) AF: 0.453 AC: 4757 AN: 10500

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31560 AN: 67912

Other (OTH) AF: 0.436 AC: 919 AN: 2110

Alfa AF: 0.451 Hom.: 34748

Bravo AF: 0.404

Asia WGS AF: 0.391 AC: 1363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.19
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs6139980; hg19: chr20-6407642;