chr6-22117206-C-T

Variant summary

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

The ENST00000444265.6(CASC15):​n.1061+6286C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0392 in 152,172 control chromosomes in the GnomAD database, including 205 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 0.039 ( 205 hom., cov: 32)

Consequence

CASC15
ENST00000444265.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.390
Variant links:
Genes affected

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=-0.9).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CASC15NR_015410.2 linkuse as main transcriptn.1422+6286C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CASC15ENST00000444265.6 linkuse as main transcriptn.1061+6286C>T intron_variant 1
CASC15ENST00000606851.5 linkuse as main transcriptn.1391+6286C>T intron_variant 2
CASC15ENST00000607048.5 linkuse as main transcriptn.1138+3169C>T intron_variant 2

Frequencies

GnomAD3 genomes
AF:
0.0392
AC:
5960
AN:
152054
Hom.:
204
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0567
Gnomad AMI
AF:
0.0493
Gnomad AMR
AF:
0.0260
Gnomad ASJ
AF:
0.00865
Gnomad EAS
AF:
0.101
Gnomad SAS
AF:
0.148
Gnomad FIN
AF:
0.0213
Gnomad MID
AF:
0.0253
Gnomad NFE
AF:
0.0237
Gnomad OTH
AF:
0.0268
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0392
AC:
5965
AN:
152172
Hom.:
205
Cov.:
32
AF XY:
0.0406
AC XY:
3020
AN XY:
74356
show subpopulations
Gnomad4 AFR
AF:
0.0567
Gnomad4 AMR
AF:
0.0259
Gnomad4 ASJ
AF:
0.00865
Gnomad4 EAS
AF:
0.101
Gnomad4 SAS
AF:
0.149
Gnomad4 FIN
AF:
0.0213
Gnomad4 NFE
AF:
0.0237
Gnomad4 OTH
AF:
0.0260
Alfa
AF:
0.0251
Hom.:
56
Bravo
AF:
0.0369
Asia WGS
AF:
0.104
AC:
361
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.23
DANN
Benign
0.62

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: rs3749995; hg19: chr6-22117435; API