rs3104746

Variant summary

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

The ENST00000510238.9(CASC16):​n.622-4326A>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 152,158 control chromosomes in the GnomAD database, including 1,080 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 ( 1080 hom., cov: 32)

Consequence

CASC16
ENST00000510238.9 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.93

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=-0.95).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CASC16NR_033920.1 linkn.605-4326A>T intron_variant Intron 2 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CASC16ENST00000510238.9 linkn.622-4326A>T intron_variant Intron 2 of 3 1
CASC16ENST00000565755.2 linkn.343-4326A>T intron_variant Intron 3 of 5 3
CASC16ENST00000652959.1 linkn.636-4326A>T intron_variant Intron 5 of 6

Frequencies

GnomAD3 genomes
AF:
0.0845
AC:
12854
AN:
152040
Hom.:
1078
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.210
Gnomad AMI
AF:
0.0187
Gnomad AMR
AF:
0.0496
Gnomad ASJ
AF:
0.0738
Gnomad EAS
AF:
0.154
Gnomad SAS
AF:
0.0527
Gnomad FIN
AF:
0.0581
Gnomad MID
AF:
0.0601
Gnomad NFE
AF:
0.0190
Gnomad OTH
AF:
0.0734
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0846
AC:
12875
AN:
152158
Hom.:
1080
Cov.:
32
AF XY:
0.0862
AC XY:
6411
AN XY:
74388
show subpopulations
African (AFR)
AF:
0.210
AC:
8713
AN:
41490
American (AMR)
AF:
0.0495
AC:
757
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
0.0738
AC:
256
AN:
3470
East Asian (EAS)
AF:
0.155
AC:
800
AN:
5160
South Asian (SAS)
AF:
0.0522
AC:
251
AN:
4812
European-Finnish (FIN)
AF:
0.0581
AC:
617
AN:
10618
Middle Eastern (MID)
AF:
0.0612
AC:
18
AN:
294
European-Non Finnish (NFE)
AF:
0.0190
AC:
1293
AN:
68006
Other (OTH)
AF:
0.0726
AC:
153
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
559
1118
1676
2235
2794
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
130
260
390
520
650
<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:
0.0578
Hom.:
86
Bravo
AF:
0.0907
Asia WGS
AF:
0.103
AC:
360
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.12
DANN
Benign
0.49
PhyloP100
-1.9

Splicing

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

Publications

Other links and lift over

dbSNP: rs3104746; hg19: chr16-52601100; API