rs3112572

Variant names:

• chr16-52566535-G-A
• rs3112572
• ENST00000510238.9:n.622-3673C>T

Variant summary

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

The ENST00000510238.9(CASC16):​n.622-3673C>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 152,016 control chromosomes in the GnomAD database, including 1,083 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 (1083 hom., cov: 32)
• Consequence: CASC16 ENST00000510238.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500
• 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=-0.95).
• 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.605-3673C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC16	ENST00000510238.9	TSL:1	n.622-3673C>T		intron	N/A
	CASC16	ENST00000565755.2	TSL:3	n.343-3673C>T		intron	N/A
	CASC16	ENST00000652959.1		n.636-3673C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0845 AC: 12842 AN: 151898 Hom.: 1081 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0497

Gnomad ASJ AF: 0.0738

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.0527

Gnomad FIN AF: 0.0575

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0190

Gnomad OTH AF: 0.0740

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

GnomAD4 genome AF: 0.0846 AC: 12863 AN: 152016 Hom.: 1083 Cov.: 32 AF XY: 0.0862 AC XY: 6404 AN XY: 74294

African (AFR) AF: 0.210 AC: 8705 AN: 41450

American (AMR) AF: 0.0496 AC: 757 AN: 15264

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

East Asian (EAS) AF: 0.156 AC: 804 AN: 5160

South Asian (SAS) AF: 0.0521 AC: 251 AN: 4816

European-Finnish (FIN) AF: 0.0575 AC: 608 AN: 10570

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

European-Non Finnish (NFE) AF: 0.0190 AC: 1293 AN: 67976

Other (OTH) AF: 0.0732 AC: 154 AN: 2104

Alfa AF: 0.0404 Hom.: 188

Bravo AF: 0.0907

Asia WGS AF: 0.104 AC: 361 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	0.21
DANN	Benign	0.66
PhyloP100		-0.0050

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3112572;

hg19: chr16-52600447;