20-6441923-G-C

Variant names:

• chr20-6441923-G-C
• rs6139993
• NR_109953.1:n.80-4800G>C

Variant summary

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

The NR_109953.1(CASC20):​n.80-4800G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 151,922 control chromosomes in the GnomAD database, including 15,700 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 0.44 (15700 hom., cov: 31)
• Consequence: CASC20 NR_109953.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 1 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CASC20	NR_109953.1	n.80-4800G>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66994 AN: 151804 Hom.: 15680 Cov.: 31

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.441 AC: 67046 AN: 151922 Hom.: 15700 Cov.: 31 AF XY: 0.443 AC XY: 32858 AN XY: 74254

African (AFR) AF: 0.303 AC: 12562 AN: 41420

American (AMR) AF: 0.614 AC: 9379 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1780 AN: 3466

East Asian (EAS) AF: 0.713 AC: 3684 AN: 5164

South Asian (SAS) AF: 0.448 AC: 2153 AN: 4804

European-Finnish (FIN) AF: 0.411 AC: 4343 AN: 10556

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31468 AN: 67918

Other (OTH) AF: 0.491 AC: 1038 AN: 2116

Alfa AF: 0.289 Hom.: 688

Bravo AF: 0.456

Asia WGS AF: 0.556 AC: 1933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.53
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs6139993; hg19: chr20-6422570;