rs1970008

Variant names:

• chr20-6487724-A-G
• rs1970008
• ENST00000415932.1:n.218+14069A>G

Your query was ambiguous. Multiple possible variants found:

• chr20-6487724-A-G
• chr20-6487724-A-T

Variant summary

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

The ENST00000415932.1(CASC20):​n.218+14069A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.716 in 152,102 control chromosomes in the GnomAD database, including 39,154 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 0.72 (39154 hom., cov: 32)
• Consequence: CASC20 ENST00000415932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.838
• Publications: 6 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CASC20	NR_109953.1	n.297+14069A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CASC20	ENST00000415932.1	n.218+14069A>G		intron_variant	Intron 2 of 2	5
CASC20	ENST00000722184.1	n.296+14069A>G		intron_variant	Intron 1 of 2
CASC20	ENST00000722185.1	n.279+3499A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108817 AN: 151984 Hom.: 39124 Cov.: 32

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.883

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.732

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.716 AC: 108888 AN: 152102 Hom.: 39154 Cov.: 32 AF XY: 0.719 AC XY: 53459 AN XY: 74336

African (AFR) AF: 0.667 AC: 27666 AN: 41492

American (AMR) AF: 0.732 AC: 11183 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.746 AC: 2587 AN: 3468

East Asian (EAS) AF: 0.883 AC: 4559 AN: 5164

South Asian (SAS) AF: 0.800 AC: 3860 AN: 4826

European-Finnish (FIN) AF: 0.728 AC: 7701 AN: 10580

Middle Eastern (MID) AF: 0.740 AC: 216 AN: 292

European-Non Finnish (NFE) AF: 0.720 AC: 48903 AN: 67968

Other (OTH) AF: 0.736 AC: 1556 AN: 2114

Alfa AF: 0.718 Hom.: 19188

Bravo AF: 0.715

Asia WGS AF: 0.849 AC: 2952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.2
DANN	Benign	0.74
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs1970008; hg19: chr20-6468371;