17-71161436-C-T

Variant names:

• chr17-71161436-C-T
• rs9747823
• ENST00000569074.1:n.134+24160G>A

Variant summary

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

The ENST00000569074.1(CASC17):​n.134+24160G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 150,584 control chromosomes in the GnomAD database, including 9,758 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 0.27 (9758 hom., cov: 33)
• Consequence: CASC17 ENST00000569074.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275
• Publications: 3 publications found

Genes affected

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

ENSG00000300845 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CASC17	NR_104152.1	n.136+24160G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CASC17	ENST00000569074.1	n.134+24160G>A		intron_variant	Intron 2 of 3	1
CASC17	ENST00000659322.1	n.142+24160G>A		intron_variant	Intron 2 of 5
CASC17	ENST00000659670.1	n.142+24160G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40289 AN: 150466 Hom.: 9729 Cov.: 33

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.0801

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.268 AC: 40362 AN: 150584 Hom.: 9758 Cov.: 33 AF XY: 0.267 AC XY: 19622 AN XY: 73512

African (AFR) AF: 0.650 AC: 26764 AN: 41144

American (AMR) AF: 0.166 AC: 2510 AN: 15096

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 534 AN: 3460

East Asian (EAS) AF: 0.0801 AC: 401 AN: 5006

South Asian (SAS) AF: 0.221 AC: 1043 AN: 4724

European-Finnish (FIN) AF: 0.156 AC: 1619 AN: 10350

Middle Eastern (MID) AF: 0.203 AC: 56 AN: 276

European-Non Finnish (NFE) AF: 0.101 AC: 6818 AN: 67536

Other (OTH) AF: 0.231 AC: 483 AN: 2088

Alfa AF: 0.148 Hom.: 5022

Bravo AF: 0.284

Asia WGS AF: 0.228 AC: 793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.8
DANN	Benign	0.75
PhyloP100		0.28
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs9747823; hg19: chr17-69157577;