20-6516136-A-T

Position:

• chr20-6516136-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.298-11058A>T 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 0.88 in 152,100 control chromosomes in the GnomAD database, including 59,017 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 (59017 hom., cov: 31)
• Consequence: CASC20 NR_109953.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.905

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=-0.9).
• 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	Protein	UniProt
CASC20	NR_109953.1	n.298-11058A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC20	ENST00000415932.1	n.219-11058A>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.880 AC: 133702 AN: 151982 Hom.: 58966 Cov.: 31

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.946

Gnomad AMR AF: 0.893

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: 0.853

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

GnomAD4 genome AF: 0.880 AC: 133807 AN: 152100 Hom.: 59017 Cov.: 31 AF XY: 0.884 AC XY: 65738 AN XY: 74348

Gnomad4 AFR AF: 0.846

Gnomad4 AMR AF: 0.894

Gnomad4 ASJ AF: 0.745

Gnomad4 EAS AF: 0.993

Gnomad4 SAS AF: 0.888

Gnomad4 FIN AF: 0.957

Gnomad4 NFE AF: 0.884

Gnomad4 OTH AF: 0.854

Alfa AF: 0.891 Hom.: 7080

Bravo AF: 0.874

Asia WGS AF: 0.919 AC: 3193 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.1
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6054326; hg19: chr20-6496783;