rs13282506

Variant summary

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

The NR_117100.1(CASC8):​n.1042-25917C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,066 control chromosomes in the GnomAD database, including 4,904 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 0.23 ( 4904 hom., cov: 32)

Consequence

CASC8
NR_117100.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.507
Variant links:
Genes affected
CASC8 (HGNC:45129): (cancer susceptibility 8)

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=-0.98).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CASC8NR_117100.1 linkuse as main transcriptn.1042-25917C>T intron_variant, non_coding_transcript_variant
CASC8NR_024393.1 linkuse as main transcriptn.1042-3160C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CASC8ENST00000502056.1 linkuse as main transcriptn.1042-3160C>T intron_variant, non_coding_transcript_variant 1
CASC8ENST00000502082.5 linkuse as main transcriptn.1042-25917C>T intron_variant, non_coding_transcript_variant 1

Frequencies

GnomAD3 genomes
AF:
0.227
AC:
34422
AN:
151948
Hom.:
4889
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0893
Gnomad AMI
AF:
0.338
Gnomad AMR
AF:
0.340
Gnomad ASJ
AF:
0.193
Gnomad EAS
AF:
0.591
Gnomad SAS
AF:
0.315
Gnomad FIN
AF:
0.300
Gnomad MID
AF:
0.196
Gnomad NFE
AF:
0.240
Gnomad OTH
AF:
0.218
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.227
AC:
34448
AN:
152066
Hom.:
4904
Cov.:
32
AF XY:
0.235
AC XY:
17482
AN XY:
74320
show subpopulations
Gnomad4 AFR
AF:
0.0891
Gnomad4 AMR
AF:
0.341
Gnomad4 ASJ
AF:
0.193
Gnomad4 EAS
AF:
0.591
Gnomad4 SAS
AF:
0.314
Gnomad4 FIN
AF:
0.300
Gnomad4 NFE
AF:
0.240
Gnomad4 OTH
AF:
0.227
Alfa
AF:
0.165
Hom.:
566
Bravo
AF:
0.222
Asia WGS
AF:
0.429
AC:
1490
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
1.2
DANN
Benign
0.65

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: rs13282506; hg19: chr8-128459125; API