chr20-6482970-C-T

Position:

• chr20-6482970-C-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+9315C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 151,110 control chromosomes in the GnomAD database, including 6,441 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 0.28 (6441 hom., cov: 31)
• Consequence: CASC20 NR_109953.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.838

Genes affected

CASC20 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CASC20	NR_109953.1	n.297+9315C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC20	ENST00000415932.1	n.218+9315C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.285 AC: 42983 AN: 150994 Hom.: 6421 Cov.: 31

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.285 AC: 43036 AN: 151110 Hom.: 6441 Cov.: 31 AF XY: 0.288 AC XY: 21221 AN XY: 73768

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.319

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.246

Alfa AF: 0.258 Hom.: 1116

Bravo AF: 0.281

Asia WGS AF: 0.267 AC: 929 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.49
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6038520; hg19: chr20-6463617;