chr16-52574351-C-G

Variant names:

• chr16-52574351-C-G
• rs3112562
• ENST00000510238.9:n.622-11489G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000510238.9(CASC16):​n.622-11489G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 151,938 control chromosomes in the GnomAD database, including 8,255 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 (8255 hom., cov: 32)
• Consequence: CASC16 ENST00000510238.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119
• Publications: 8 publications found

Genes affected

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

ENSG00000285800 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CASC16	NR_033920.1	n.605-11489G>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CASC16	ENST00000510238.9	n.622-11489G>C		intron_variant	Intron 2 of 3	1
CASC16	ENST00000563844.1	n.445-1007G>C		intron_variant	Intron 4 of 4	3
CASC16	ENST00000565755.2	n.343-11489G>C		intron_variant	Intron 3 of 5	3

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46511 AN: 151820 Hom.: 8235 Cov.: 32

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.307 AC: 46575 AN: 151938 Hom.: 8255 Cov.: 32 AF XY: 0.300 AC XY: 22313 AN XY: 74264

African (AFR) AF: 0.495 AC: 20486 AN: 41400

American (AMR) AF: 0.257 AC: 3926 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 956 AN: 3472

East Asian (EAS) AF: 0.314 AC: 1617 AN: 5154

South Asian (SAS) AF: 0.247 AC: 1185 AN: 4792

European-Finnish (FIN) AF: 0.188 AC: 1989 AN: 10572

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15491 AN: 67968

Other (OTH) AF: 0.298 AC: 629 AN: 2108

Alfa AF: 0.271 Hom.: 784

Bravo AF: 0.319

Asia WGS AF: 0.277 AC: 967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.63
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs3112562; hg19: chr16-52608263;