rs853600

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000435944.5(CASC2):​n.453-66886C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 151,882 control chromosomes in the GnomAD database, including 18,153 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 ( 18153 hom., cov: 31)

Consequence

CASC2
ENST00000435944.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.40
Variant links:
Genes affected
CASC2 (HGNC:22933): (cancer susceptibility 2) Involved in defense response to tumor cell; negative regulation of MAPK cascade; and positive regulation of cysteine-type endopeptidase activity involved in apoptotic process. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.01).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CASC2NR_026939.1 linkn.456-66886C>A intron_variant Intron 3 of 4
CASC2NR_026940.1 linkn.456-67800C>A intron_variant Intron 3 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CASC2ENST00000435944.5 linkn.453-66886C>A intron_variant Intron 3 of 4 1
CASC2ENST00000414722.5 linkn.542-66886C>A intron_variant Intron 3 of 3 5
CASC2ENST00000439517.2 linkn.155-66886C>A intron_variant Intron 2 of 3 5

Frequencies

GnomAD3 genomes
AF:
0.453
AC:
68697
AN:
151764
Hom.:
18149
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.204
Gnomad AMI
AF:
0.489
Gnomad AMR
AF:
0.413
Gnomad ASJ
AF:
0.516
Gnomad EAS
AF:
0.148
Gnomad SAS
AF:
0.580
Gnomad FIN
AF:
0.634
Gnomad MID
AF:
0.491
Gnomad NFE
AF:
0.594
Gnomad OTH
AF:
0.476
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.452
AC:
68715
AN:
151882
Hom.:
18153
Cov.:
31
AF XY:
0.452
AC XY:
33541
AN XY:
74210
show subpopulations
Gnomad4 AFR
AF:
0.204
Gnomad4 AMR
AF:
0.413
Gnomad4 ASJ
AF:
0.516
Gnomad4 EAS
AF:
0.148
Gnomad4 SAS
AF:
0.581
Gnomad4 FIN
AF:
0.634
Gnomad4 NFE
AF:
0.594
Gnomad4 OTH
AF:
0.477
Alfa
AF:
0.567
Hom.:
11434
Bravo
AF:
0.420
Asia WGS
AF:
0.380
AC:
1325
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.016
DANN
Benign
0.26

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs853600; hg19: chr10-119899147; API