16-52565276-C-T

Variant summary

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

The NR_033920.1(CASC16):n.605-2414G>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 0.2 in 152,100 control chromosomes in the GnomAD database, including 3,615 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 0.20 (3615 hom., cov: 33)
• Consequence: CASC16 NR_033920.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

Genes affected

CASC16 (HGNC:48608): (cancer susceptibility 16)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CASC16	NR_033920.1	n.605-2414G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CASC16	ENST00000510238.8	n.615-2414G>A		intron_variant, non_coding_transcript_variant		1
CASC16	ENST00000652959.1	n.636-2414G>A		intron_variant, non_coding_transcript_variant
CASC16	ENST00000671536.1	n.622-12842G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30401 AN: 151982 Hom.: 3609 Cov.: 33

Gnomad AFR AF: 0.0653

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.200 AC: 30427 AN: 152100 Hom.: 3615 Cov.: 33 AF XY: 0.203 AC XY: 15067 AN XY: 74336

Gnomad4 AFR AF: 0.0652

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.246

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.238

Alfa AF: 0.235 Hom.: 5784

Bravo AF: 0.199

Asia WGS AF: 0.227 AC: 792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	2.8
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4784227; hg19: chr16-52599188;