17-71194808-T-C

Position:

• chr17-71194808-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

CASC17 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CASC17	NR_104152.1	n.76+7296A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC17	ENST00000569074.1	n.74+7296A>G		intron_variant		1
CASC17	ENST00000659322.1	n.82+7296A>G		intron_variant
CASC17	ENST00000659670.1	n.82+7296A>G		intron_variant

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

Gnomad4 AFR AF: 0.831

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.440

Gnomad4 EAS AF: 0.444

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.559

Gnomad4 OTH AF: 0.566

Alfa AF: 0.552 Hom.: 33588

Bravo AF: 0.627

Asia WGS AF: 0.540 AC: 1878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7214479; hg19: chr17-69190949;