20-6468031-T-G

Position:

• chr20-6468031-T-G

Variant summary

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

The NR_109953.1(CASC20):​n.181-5508T>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 0.804 in 152,100 control chromosomes in the GnomAD database, including 49,327 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 0.80 (49327 hom., cov: 33)
• Consequence: CASC20 NR_109953.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CASC20	NR_109953.1	n.181-5508T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CASC20	ENST00000415932.1	n.102-5508T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.804 AC: 122179 AN: 151982 Hom.: 49280 Cov.: 33

Gnomad AFR AF: 0.874

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.862

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.804 AC: 122281 AN: 152100 Hom.: 49327 Cov.: 33 AF XY: 0.803 AC XY: 59681 AN XY: 74336

Gnomad4 AFR AF: 0.874

Gnomad4 AMR AF: 0.805

Gnomad4 ASJ AF: 0.799

Gnomad4 EAS AF: 0.862

Gnomad4 SAS AF: 0.816

Gnomad4 FIN AF: 0.727

Gnomad4 NFE AF: 0.768

Gnomad4 OTH AF: 0.824

Alfa AF: 0.777 Hom.: 62074

Bravo AF: 0.813

Asia WGS AF: 0.852 AC: 2963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6117277; hg19: chr20-6448678;