rs3112623

Variant names:

• chr16-52593614-A-G
• rs3112623
• ENST00000510238.9:n.490-2547T>C

Your query was ambiguous. Multiple possible variants found:

• chr16-52593614-A-G
• chr16-52593614-A-T

Variant summary

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

The ENST00000510238.9(CASC16):​n.490-2547T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 152,044 control chromosomes in the GnomAD database, including 15,553 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 0.44 (15553 hom., cov: 33)
• Consequence: CASC16 ENST00000510238.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.08
• Publications: 5 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CASC16	NR_033920.1	n.473-2547T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CASC16	ENST00000510238.9	n.490-2547T>C		intron_variant	Intron 1 of 3	1
CASC16	ENST00000563844.1	n.313-2547T>C		intron_variant	Intron 3 of 4	3
CASC16	ENST00000565755.2	n.211-2547T>C		intron_variant	Intron 2 of 5	3

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67448 AN: 151926 Hom.: 15533 Cov.: 33

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.444 AC: 67516 AN: 152044 Hom.: 15553 Cov.: 33 AF XY: 0.443 AC XY: 32951 AN XY: 74312

African (AFR) AF: 0.413 AC: 17107 AN: 41460

American (AMR) AF: 0.536 AC: 8194 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1826 AN: 3472

East Asian (EAS) AF: 0.783 AC: 4042 AN: 5164

South Asian (SAS) AF: 0.456 AC: 2197 AN: 4818

European-Finnish (FIN) AF: 0.362 AC: 3815 AN: 10552

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

European-Non Finnish (NFE) AF: 0.422 AC: 28665 AN: 67980

Other (OTH) AF: 0.502 AC: 1060 AN: 2110

Alfa AF: 0.440 Hom.: 9977

Bravo AF: 0.457

Asia WGS AF: 0.577 AC: 2007 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.5
DANN	Benign	0.84
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs3112623; hg19: chr16-52627526;