chr16-52567188-T-A

Variant names:

• chr16-52567188-T-A
• rs3104746
• ENST00000510238.9:n.622-4326A>T

Variant summary

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

The ENST00000510238.9(CASC16):​n.622-4326A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0846 in 152,158 control chromosomes in the GnomAD database, including 1,080 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 0.085 (1080 hom., cov: 32)
• Consequence: CASC16 ENST00000510238.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 10 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 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.605-4326A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC16	ENST00000510238.9	TSL:1	n.622-4326A>T		intron	N/A
	CASC16	ENST00000565755.2	TSL:3	n.343-4326A>T		intron	N/A
	CASC16	ENST00000652959.1		n.636-4326A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0845 AC: 12854 AN: 152040 Hom.: 1078 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.0187

Gnomad AMR AF: 0.0496

Gnomad ASJ AF: 0.0738

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.0527

Gnomad FIN AF: 0.0581

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0190

Gnomad OTH AF: 0.0734

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

GnomAD4 genome AF: 0.0846 AC: 12875 AN: 152158 Hom.: 1080 Cov.: 32 AF XY: 0.0862 AC XY: 6411 AN XY: 74388

African (AFR) AF: 0.210 AC: 8713 AN: 41490

American (AMR) AF: 0.0495 AC: 757 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0738 AC: 256 AN: 3470

East Asian (EAS) AF: 0.155 AC: 800 AN: 5160

South Asian (SAS) AF: 0.0522 AC: 251 AN: 4812

European-Finnish (FIN) AF: 0.0581 AC: 617 AN: 10618

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0190 AC: 1293 AN: 68006

Other (OTH) AF: 0.0726 AC: 153 AN: 2106

Alfa AF: 0.0578 Hom.: 86

Bravo AF: 0.0907

Asia WGS AF: 0.103 AC: 360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.12
DANN	Benign	0.49
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs3104746; hg19: chr16-52601100;