17-71139490-G-A

Variant names:

• chr17-71139490-G-A
• rs9900242
• ENST00000569074.1:n.135-7020C>T

Variant summary

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

The ENST00000569074.1(CASC17):​n.135-7020C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 152,014 control chromosomes in the GnomAD database, including 8,295 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 0.32 (8295 hom., cov: 32)
• Consequence: CASC17 ENST00000569074.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.332
• Publications: 4 publications found

Genes affected

CASC17 (HGNC:43911): (cancer susceptibility 17)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000569074.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC17	NR_104152.1		n.137-7020C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC17	ENST00000569074.1	TSL:1	n.135-7020C>T		intron	N/A
	CASC17	ENST00000659322.1		n.143-2480C>T		intron	N/A
	CASC17	ENST00000659670.1		n.143-7020C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48842 AN: 151896 Hom.: 8290 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.321 AC: 48869 AN: 152014 Hom.: 8295 Cov.: 32 AF XY: 0.317 AC XY: 23528 AN XY: 74278

African (AFR) AF: 0.214 AC: 8866 AN: 41496

American (AMR) AF: 0.330 AC: 5033 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 796 AN: 3468

East Asian (EAS) AF: 0.430 AC: 2216 AN: 5156

South Asian (SAS) AF: 0.239 AC: 1150 AN: 4818

European-Finnish (FIN) AF: 0.331 AC: 3495 AN: 10554

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.388 AC: 26389 AN: 67936

Other (OTH) AF: 0.293 AC: 617 AN: 2108

Alfa AF: 0.366 Hom.: 18251

Bravo AF: 0.319

Asia WGS AF: 0.321 AC: 1119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
DANN	Benign	0.34
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs9900242; hg19: chr17-69135631;