17-71111986-T-C

Variant names:

• chr17-71111986-T-C
• rs984434
• ENST00000569074.1:n.216-12368A>G

Variant summary

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

The ENST00000569074.1(CASC17):​n.216-12368A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.59 in 151,952 control chromosomes in the GnomAD database, including 27,753 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 0.59 (27753 hom., cov: 31)
• Consequence: CASC17 ENST00000569074.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540
• Publications: 11 publications found

Genes affected

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

ENSG00000300867 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.787 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.218-12368A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC17	ENST00000569074.1	TSL:1	n.216-12368A>G		intron	N/A
	CASC17	ENST00000659322.1		n.556-12368A>G		intron	N/A
	CASC17	ENST00000659670.1		n.252-12368A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89620 AN: 151834 Hom.: 27724 Cov.: 31

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.590 AC: 89688 AN: 151952 Hom.: 27753 Cov.: 31 AF XY: 0.585 AC XY: 43450 AN XY: 74262

African (AFR) AF: 0.794 AC: 32928 AN: 41454

American (AMR) AF: 0.478 AC: 7305 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1565 AN: 3472

East Asian (EAS) AF: 0.627 AC: 3231 AN: 5152

South Asian (SAS) AF: 0.448 AC: 2159 AN: 4816

European-Finnish (FIN) AF: 0.501 AC: 5275 AN: 10538

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.522 AC: 35433 AN: 67928

Other (OTH) AF: 0.535 AC: 1131 AN: 2114

Alfa AF: 0.530 Hom.: 11137

Bravo AF: 0.601

Asia WGS AF: 0.575 AC: 2002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.82
DANN	Benign	0.49
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs984434; hg19: chr17-69108127;