rs9900242

Positions:

• chr17-71139490-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_104152.1(CASC17):​n.137-7020C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 152,014 control chromosomes in the GnomAD database, including 8,295 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 0.32 (8295 hom., cov: 32)
• Consequence: CASC17 NR_104152.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.332

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CASC17	NR_104152.1	n.137-7020C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CASC17	ENST00000659670.1	n.143-7020C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48842 AN: 151896 Hom.: 8290 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.321 AC: 48869 AN: 152014 Hom.: 8295 Cov.: 32 AF XY: 0.317 AC XY: 23528 AN XY: 74278

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.293

Alfa AF: 0.365 Hom.: 13433

Bravo AF: 0.319

Asia WGS AF: 0.321 AC: 1119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9900242; hg19: chr17-69135631;