17-71112612-G-T

Position:

• chr17-71112612-G-T

Variant summary

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

The NR_104152.1(CASC17):​n.218-12994C>A 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 0.56 in 151,984 control chromosomes in the GnomAD database, including 24,465 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 0.56 (24465 hom., cov: 32)
• Consequence: CASC17 NR_104152.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CASC17	NR_104152.1	n.218-12994C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC17	ENST00000659670.1	n.252-12994C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85073 AN: 151866 Hom.: 24444 Cov.: 32

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.560 AC: 85130 AN: 151984 Hom.: 24465 Cov.: 32 AF XY: 0.556 AC XY: 41255 AN XY: 74258

Gnomad4 AFR AF: 0.693

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.624

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.499

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.509

Alfa AF: 0.522 Hom.: 46125

Bravo AF: 0.565

Asia WGS AF: 0.572 AC: 1990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1859962; hg19: chr17-69108753;