rs1411296

chr20-6508363-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_109953.1(CASC20):n.298-18831C>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.881 in 152,140 control chromosomes in the GnomAD database, including 59,195 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 (59195 hom., cov: 31)
• Consequence: CASC20 NR_109953.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.529

Genes affected

CASC20 (HGNC:49477): (cancer susceptibility 20)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CASC20	NR_109953.1	n.298-18831C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CASC20	ENST00000415932.1	n.219-18831C>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.881 AC: 133923 AN: 152022 Hom.: 59143 Cov.: 31

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.946

Gnomad AMR AF: 0.895

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: 0.854

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

GnomAD4 genome AF: 0.881 AC: 134029 AN: 152140 Hom.: 59195 Cov.: 31 AF XY: 0.885 AC XY: 65836 AN XY: 74372

Gnomad4 AFR AF: 0.849

Gnomad4 AMR AF: 0.895

Gnomad4 ASJ AF: 0.745

Gnomad4 EAS AF: 0.993

Gnomad4 SAS AF: 0.887

Gnomad4 FIN AF: 0.957

Gnomad4 NFE AF: 0.884

Gnomad4 OTH AF: 0.855

Alfa AF: 0.891 Hom.: 7526

Bravo AF: 0.876

Asia WGS AF: 0.920 AC: 3193 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.1
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1411296; hg19: chr20-6489010;