chr17-71111675-A-G

Variant names:

• chr17-71111675-A-G
• rs8072254
• ENST00000569074.1:n.216-12057T>C

Variant summary

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

The ENST00000569074.1(CASC17):​n.216-12057T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.605 in 152,018 control chromosomes in the GnomAD database, including 29,542 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 0.60 (29542 hom., cov: 32)
• Consequence: CASC17 ENST00000569074.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.439
• Publications: 21 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=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.837 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.218-12057T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC17	ENST00000569074.1	TSL:1	n.216-12057T>C		intron	N/A
	CASC17	ENST00000659322.1		n.556-12057T>C		intron	N/A
	CASC17	ENST00000659670.1		n.252-12057T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91836 AN: 151900 Hom.: 29505 Cov.: 32

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.605 AC: 91912 AN: 152018 Hom.: 29542 Cov.: 32 AF XY: 0.598 AC XY: 44462 AN XY: 74326

African (AFR) AF: 0.844 AC: 35019 AN: 41468

American (AMR) AF: 0.482 AC: 7365 AN: 15270

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

East Asian (EAS) AF: 0.628 AC: 3241 AN: 5162

South Asian (SAS) AF: 0.449 AC: 2160 AN: 4812

European-Finnish (FIN) AF: 0.499 AC: 5275 AN: 10562

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

European-Non Finnish (NFE) AF: 0.522 AC: 35475 AN: 67958

Other (OTH) AF: 0.545 AC: 1150 AN: 2110

Alfa AF: 0.546 Hom.: 10811

Bravo AF: 0.617

Asia WGS AF: 0.583 AC: 2030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	16
DANN	Benign	0.71
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs8072254; hg19: chr17-69107816;