rs8077906

Variant names:

• chr17-71116092-G-A
• rs8077906
• ENST00000569074.1:n.215+16298C>T

Variant summary

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

The ENST00000569074.1(CASC17):​n.215+16298C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 151,880 control chromosomes in the GnomAD database, including 9,948 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 0.36 (9948 hom., cov: 32)
• Consequence: CASC17 ENST00000569074.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450
• Publications: 6 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.527 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.217+16298C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC17	ENST00000569074.1	TSL:1	n.215+16298C>T		intron	N/A
	CASC17	ENST00000659322.1		n.555+16298C>T		intron	N/A
	CASC17	ENST00000659670.1		n.251+16270C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54400 AN: 151762 Hom.: 9944 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.358 AC: 54426 AN: 151880 Hom.: 9948 Cov.: 32 AF XY: 0.354 AC XY: 26261 AN XY: 74212

African (AFR) AF: 0.396 AC: 16413 AN: 41430

American (AMR) AF: 0.308 AC: 4696 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 850 AN: 3464

East Asian (EAS) AF: 0.543 AC: 2801 AN: 5154

South Asian (SAS) AF: 0.197 AC: 947 AN: 4814

European-Finnish (FIN) AF: 0.332 AC: 3503 AN: 10564

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24295 AN: 67890

Other (OTH) AF: 0.308 AC: 648 AN: 2106

Alfa AF: 0.351 Hom.: 4953

Bravo AF: 0.362

Asia WGS AF: 0.345 AC: 1200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.6
DANN	Benign	0.70
PhyloP100		0.045

Splicing

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

Other links and lift over

dbSNP: rs8077906; hg19: chr17-69112233;