ENST00000510238.8:n.615-2414G>A

Variant names:

• chr16-52565276-C-T
• rs4784227
• ENST00000510238.9:n.622-2414G>A

Variant summary

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

The ENST00000510238.9(CASC16):​n.622-2414G>A variant causes a intron 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 ENST00000510238.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 143 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=-0.74).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000510238.9. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC16	NR_033920.1		n.605-2414G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC16	ENST00000510238.9	TSL:1	n.622-2414G>A		intron	N/A
	CASC16	ENST00000565755.2	TSL:3	n.343-2414G>A		intron	N/A
	CASC16	ENST00000652959.1		n.636-2414G>A		intron	N/A

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

African (AFR) AF: 0.0652 AC: 2707 AN: 41506

American (AMR) AF: 0.293 AC: 4472 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1058 AN: 3468

East Asian (EAS) AF: 0.246 AC: 1274 AN: 5176

South Asian (SAS) AF: 0.209 AC: 1007 AN: 4820

European-Finnish (FIN) AF: 0.250 AC: 2642 AN: 10558

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16428 AN: 67972

Other (OTH) AF: 0.238 AC: 504 AN: 2114

Alfa AF: 0.229 Hom.: 14323

Bravo AF: 0.199

Asia WGS AF: 0.227 AC: 792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	2.8
DANN	Benign	0.76
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4784227; hg19: chr16-52599188;