17-71194808-T-C

Variant names:

• chr17-71194808-T-C
• rs7214479
• ENST00000569074.1:n.74+7296A>G

Variant summary

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

The ENST00000569074.1(CASC17):​n.74+7296A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 152,014 control chromosomes in the GnomAD database, including 30,215 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 0.62 (30215 hom., cov: 32)
• Consequence: CASC17 ENST00000569074.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 9 publications found

Genes affected

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

ENSG00000300893 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.824 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC17	NR_104152.1		n.76+7296A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC17	ENST00000569074.1	TSL:1	n.74+7296A>G		intron	N/A
	CASC17	ENST00000659322.1		n.82+7296A>G		intron	N/A
	CASC17	ENST00000659670.1		n.82+7296A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93406 AN: 151896 Hom.: 30171 Cov.: 32

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.615 AC: 93499 AN: 152014 Hom.: 30215 Cov.: 32 AF XY: 0.607 AC XY: 45077 AN XY: 74316

African (AFR) AF: 0.831 AC: 34511 AN: 41508

American (AMR) AF: 0.519 AC: 7926 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1522 AN: 3462

East Asian (EAS) AF: 0.444 AC: 2291 AN: 5158

South Asian (SAS) AF: 0.487 AC: 2344 AN: 4818

European-Finnish (FIN) AF: 0.485 AC: 5129 AN: 10566

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.559 AC: 37969 AN: 67922

Other (OTH) AF: 0.566 AC: 1195 AN: 2110

Alfa AF: 0.560 Hom.: 48059

Bravo AF: 0.627

Asia WGS AF: 0.540 AC: 1878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.99
DANN	Benign	0.50
PhyloP100		-1.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7214479;

hg19: chr17-69190949;