rs11654749

chr17-71129465-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.217+2925C>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 0.306 in 151,948 control chromosomes in the GnomAD database, including 7,833 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 0.31 (7833 hom., cov: 32)
• Consequence: CASC17 NR_104152.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CASC17	NR_104152.1	n.217+2925C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CASC17	ENST00000659670.1	n.251+2897C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46503 AN: 151828 Hom.: 7830 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.306 AC: 46525 AN: 151948 Hom.: 7833 Cov.: 32 AF XY: 0.302 AC XY: 22427 AN XY: 74262

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.432

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.279

Alfa AF: 0.355 Hom.: 2398

Bravo AF: 0.301

Asia WGS AF: 0.320 AC: 1107 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	2.4
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11654749; hg19: chr17-69125606;