17-71111986-T-C

Position:

• chr17-71111986-T-C

Variant summary

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

The ENST00000569074.1(CASC17):​n.216-12368A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.59 in 151,952 control chromosomes in the GnomAD database, including 27,753 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 0.59 (27753 hom., cov: 31)
• Consequence: CASC17 ENST00000569074.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540

Genes affected

CASC17 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CASC17	NR_104152.1	n.218-12368A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC17	ENST00000569074.1	n.216-12368A>G		intron_variant		1
CASC17	ENST00000659322.1	n.556-12368A>G		intron_variant
CASC17	ENST00000659670.1	n.252-12368A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89620 AN: 151834 Hom.: 27724 Cov.: 31

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.590 AC: 89688 AN: 151952 Hom.: 27753 Cov.: 31 AF XY: 0.585 AC XY: 43450 AN XY: 74262

Gnomad4 AFR AF: 0.794

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.627

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.522

Gnomad4 OTH AF: 0.535

Alfa AF: 0.516 Hom.: 5764

Bravo AF: 0.601

Asia WGS AF: 0.575 AC: 2002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.82
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs984434; hg19: chr17-69108127;