rs3112612

Variant names:

• chr16-52601252-G-A
• rs3112612
• ENST00000510238.9:n.489+5252C>T

Your query was ambiguous. Multiple possible variants found:

• chr16-52601252-G-A
• chr16-52601252-G-C
• chr16-52601252-G-T

Variant summary

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

The ENST00000510238.9(CASC16):​n.489+5252C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 151,978 control chromosomes in the GnomAD database, including 15,843 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 0.45 (15843 hom., cov: 32)
• Consequence: CASC16 ENST00000510238.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189
• Publications: 53 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.763 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.472+5252C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC16	ENST00000510238.9	TSL:1	n.489+5252C>T		intron	N/A
	CASC16	ENST00000563844.1	TSL:3	n.313-10185C>T		intron	N/A
	CASC16	ENST00000565755.2	TSL:3	n.210+5252C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68111 AN: 151860 Hom.: 15823 Cov.: 32

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.449 AC: 68178 AN: 151978 Hom.: 15843 Cov.: 32 AF XY: 0.448 AC XY: 33260 AN XY: 74288

African (AFR) AF: 0.424 AC: 17581 AN: 41424

American (AMR) AF: 0.540 AC: 8245 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1883 AN: 3470

East Asian (EAS) AF: 0.783 AC: 4041 AN: 5160

South Asian (SAS) AF: 0.456 AC: 2194 AN: 4810

European-Finnish (FIN) AF: 0.363 AC: 3841 AN: 10570

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28718 AN: 67966

Other (OTH) AF: 0.505 AC: 1065 AN: 2110

Alfa AF: 0.441 Hom.: 71749

Bravo AF: 0.462

Asia WGS AF: 0.576 AC: 2007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.43
PhyloP100		-0.19

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: rs3112612;

hg19: chr16-52635164;