16-52591640-A-G

Variant summary

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

The ENST00000510238.9(CASC16):​n.490-573T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 151,926 control chromosomes in the GnomAD database, including 17,986 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 0.48 ( 17986 hom., cov: 32)

Consequence

CASC16
ENST00000510238.9 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.28

Publications

10 publications found
Variant links:
Genes affected
CASC16 (HGNC:48608): (cancer susceptibility 16)

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=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CASC16NR_033920.1 linkn.473-573T>C intron_variant Intron 1 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CASC16ENST00000510238.9 linkn.490-573T>C intron_variant Intron 1 of 3 1
CASC16ENST00000826549.1 linkn.358T>C non_coding_transcript_exon_variant Exon 1 of 4
CASC16ENST00000826550.1 linkn.291T>C non_coding_transcript_exon_variant Exon 1 of 3

Frequencies

GnomAD3 genomes
AF:
0.478
AC:
72524
AN:
151808
Hom.:
17949
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.528
Gnomad AMI
AF:
0.480
Gnomad AMR
AF:
0.551
Gnomad ASJ
AF:
0.529
Gnomad EAS
AF:
0.784
Gnomad SAS
AF:
0.458
Gnomad FIN
AF:
0.363
Gnomad MID
AF:
0.608
Gnomad NFE
AF:
0.422
Gnomad OTH
AF:
0.518
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.478
AC:
72616
AN:
151926
Hom.:
17986
Cov.:
32
AF XY:
0.475
AC XY:
35282
AN XY:
74224
show subpopulations
African (AFR)
AF:
0.528
AC:
21881
AN:
41428
American (AMR)
AF:
0.552
AC:
8418
AN:
15258
Ashkenazi Jewish (ASJ)
AF:
0.529
AC:
1833
AN:
3468
East Asian (EAS)
AF:
0.784
AC:
4029
AN:
5138
South Asian (SAS)
AF:
0.459
AC:
2207
AN:
4812
European-Finnish (FIN)
AF:
0.363
AC:
3825
AN:
10548
Middle Eastern (MID)
AF:
0.599
AC:
176
AN:
294
European-Non Finnish (NFE)
AF:
0.422
AC:
28709
AN:
67964
Other (OTH)
AF:
0.523
AC:
1103
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1906
3812
5718
7624
9530
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
652
1304
1956
2608
3260
<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:
0.446
Hom.:
33209
Bravo
AF:
0.496
Asia WGS
AF:
0.588
AC:
2047
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.015
DANN
Benign
0.42
PhyloP100
-1.3

Splicing

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

Publications

Other links and lift over

dbSNP: rs3112625; hg19: chr16-52625552; API