dbSNP rs3112612: CASC16:n.489+5252C>T (chr16-52601252-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.189

Publications

53 publications found

Variant links:

Genes affected

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

CASC16 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CASC16	NR_033920.1 link	n.472+5252C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CASC16	ENST00000510238.9 link	n.489+5252C>T	intron_variant	Intron 1 of 3	1
CASC16	ENST00000563844.1 link	n.313-10185C>T	intron_variant	Intron 3 of 4	3
CASC16	ENST00000565755.2 link	n.210+5252C>T	intron_variant	Intron 2 of 5	3

Frequencies

GnomAD3 genomes

AF:

0.449

AC:

68111

AN:

151860

Hom.:

15823

Cov.:

show subpopulations

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.:

AF XY:

0.448

AC XY:

33260

AN XY:

74288

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1901

3803

5704

7606

9507

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

630

1260

1890

2520

3150

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.0

(source)

DANN

Benign

0.43

PhyloP100

-0.19

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over