rs6054303

chr20-6482865-A-Gchr20-6482865-A-T

Variant summary

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

The NR_109953.1(CASC20):n.297+9210A>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 0.286 in 151,948 control chromosomes in the GnomAD database, including 6,538 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 0.29 (6538 hom., cov: 32)
• Consequence: CASC20 NR_109953.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.753

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CASC20	NR_109953.1	n.297+9210A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CASC20	ENST00000415932.1	n.218+9210A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43411 AN: 151830 Hom.: 6519 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.286 AC: 43464 AN: 151948 Hom.: 6538 Cov.: 32 AF XY: 0.289 AC XY: 21444 AN XY: 74252

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.246

Alfa AF: 0.175 Hom.: 461

Bravo AF: 0.282

Asia WGS AF: 0.268 AC: 934 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	9.7
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6054303; hg19: chr20-6463512;