rs9940048

Variant summary

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

The ENST00000652959.1(CASC16):​n.339+1001C>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 0.263 in 151,678 control chromosomes in the GnomAD database, including 5,409 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 0.26 ( 5409 hom., cov: 32)
Exomes 𝑓: 0.50 ( 0 hom. )

Consequence

CASC16
ENST00000652959.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.566
Variant links:
Genes affected
CASC16 (HGNC:48608): (cancer susceptibility 16)

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=-0.71).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CASC16ENST00000652959.1 linkuse as main transcriptn.339+1001C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.263
AC:
39925
AN:
151556
Hom.:
5406
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.303
Gnomad AMI
AF:
0.227
Gnomad AMR
AF:
0.235
Gnomad ASJ
AF:
0.357
Gnomad EAS
AF:
0.257
Gnomad SAS
AF:
0.223
Gnomad FIN
AF:
0.207
Gnomad MID
AF:
0.370
Gnomad NFE
AF:
0.253
Gnomad OTH
AF:
0.287
GnomAD4 exome
AF:
0.500
AC:
3
AN:
6
Hom.:
0
Cov.:
0
AF XY:
0.500
AC XY:
2
AN XY:
4
show subpopulations
Gnomad4 NFE exome
AF:
0.500
GnomAD4 genome
AF:
0.263
AC:
39944
AN:
151672
Hom.:
5409
Cov.:
32
AF XY:
0.259
AC XY:
19175
AN XY:
74098
show subpopulations
Gnomad4 AFR
AF:
0.302
Gnomad4 AMR
AF:
0.235
Gnomad4 ASJ
AF:
0.357
Gnomad4 EAS
AF:
0.257
Gnomad4 SAS
AF:
0.224
Gnomad4 FIN
AF:
0.207
Gnomad4 NFE
AF:
0.253
Gnomad4 OTH
AF:
0.285
Alfa
AF:
0.263
Hom.:
488
Bravo
AF:
0.267
Asia WGS
AF:
0.226
AC:
787
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.71
CADD
Benign
15
DANN
Benign
0.76

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: rs9940048; hg19: chr16-52663861; API