chr20-6516136-A-T

Variant names:

• chr20-6516136-A-T
• rs6054326
• ENST00000415932.1:n.219-11058A>T

Variant summary

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

The NR_109953.1(CASC20):​n.298-11058A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.88 in 152,100 control chromosomes in the GnomAD database, including 59,017 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 0.88 (59017 hom., cov: 31)
• Consequence: CASC20 NR_109953.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.905
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 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.298-11058A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC20	ENST00000415932.1	TSL:5	n.219-11058A>T		intron	N/A
	CASC20	ENST00000722184.1		n.296+42481A>T		intron	N/A
	CASC20	ENST00000722185.1		n.279+31911A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.880 AC: 133702 AN: 151982 Hom.: 58966 Cov.: 31

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.946

Gnomad AMR AF: 0.893

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.957

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.884

Gnomad OTH AF: 0.853

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

GnomAD4 genome AF: 0.880 AC: 133807 AN: 152100 Hom.: 59017 Cov.: 31 AF XY: 0.884 AC XY: 65738 AN XY: 74348

African (AFR) AF: 0.846 AC: 35087 AN: 41498

American (AMR) AF: 0.894 AC: 13635 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.745 AC: 2583 AN: 3468

East Asian (EAS) AF: 0.993 AC: 5140 AN: 5178

South Asian (SAS) AF: 0.888 AC: 4275 AN: 4816

European-Finnish (FIN) AF: 0.957 AC: 10155 AN: 10614

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.884 AC: 60040 AN: 67950

Other (OTH) AF: 0.854 AC: 1804 AN: 2112

Alfa AF: 0.891 Hom.: 7080

Bravo AF: 0.874

Asia WGS AF: 0.919 AC: 3193 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.1
DANN	Benign	0.73
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs6054326; hg19: chr20-6496783;