6-91604261-T-G

Variant summary

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

The ENST00000656997.1(CASC6):​n.717+19838A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 152,082 control chromosomes in the GnomAD database, including 10,784 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 0.36 ( 10784 hom., cov: 33)

Consequence

CASC6
ENST00000656997.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.308
Variant links:
Genes affected
CASC6 (HGNC:49076): (cancer susceptibility 6)

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=-0.93).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CASC6ENST00000656997.1 linkn.717+19838A>C intron_variant Intron 2 of 3

Frequencies

GnomAD3 genomes
AF:
0.365
AC:
55433
AN:
151964
Hom.:
10786
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.284
Gnomad AMI
AF:
0.225
Gnomad AMR
AF:
0.439
Gnomad ASJ
AF:
0.294
Gnomad EAS
AF:
0.706
Gnomad SAS
AF:
0.485
Gnomad FIN
AF:
0.450
Gnomad MID
AF:
0.361
Gnomad NFE
AF:
0.356
Gnomad OTH
AF:
0.336
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.365
AC:
55438
AN:
152082
Hom.:
10784
Cov.:
33
AF XY:
0.376
AC XY:
27965
AN XY:
74334
show subpopulations
Gnomad4 AFR
AF:
0.283
Gnomad4 AMR
AF:
0.439
Gnomad4 ASJ
AF:
0.294
Gnomad4 EAS
AF:
0.706
Gnomad4 SAS
AF:
0.486
Gnomad4 FIN
AF:
0.450
Gnomad4 NFE
AF:
0.356
Gnomad4 OTH
AF:
0.334
Alfa
AF:
0.359
Hom.:
20289
Bravo
AF:
0.362
Asia WGS
AF:
0.526
AC:
1825
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.97
DANN
Benign
0.60

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: rs9353859; hg19: chr6-92313979; COSMIC: COSV60245798; API