dbSNP rs9900242: CASC17:n.135-7020C>T (chr17-71139490-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000569074.1(CASC17):n.135-7020C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 152,014 control chromosomes in the GnomAD database, including 8,295 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 0.32 ( 8295 hom., cov: 32)

Consequence

CASC17
ENST00000569074.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.332

Publications

4 publications found

Variant links:

Genes affected

CASC17 (HGNC:43911): (cancer susceptibility 17)

CASC17 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.01).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CASC17	NR_104152.1 link	n.137-7020C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CASC17	ENST00000569074.1 link	n.135-7020C>T	intron_variant	Intron 2 of 3	1
CASC17	ENST00000659322.1 link	n.143-2480C>T	intron_variant	Intron 2 of 5
CASC17	ENST00000659670.1 link	n.143-7020C>T	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.322

AC:

48842

AN:

151896

Hom.:

8290

Cov.:

show subpopulations

Gnomad AFR

AF:

0.214

Gnomad AMI

AF:

0.280

Gnomad AMR

AF:

0.329

Gnomad ASJ

AF:

0.230

Gnomad EAS

AF:

0.430

Gnomad SAS

AF:

0.238

Gnomad FIN

AF:

0.331

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.388

Gnomad OTH

AF:

0.295

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.321

AC:

48869

AN:

152014

Hom.:

8295

Cov.:

AF XY:

0.317

AC XY:

23528

AN XY:

74278

show subpopulations

African (AFR)

AF:

0.214

AC:

8866

AN:

41496

American (AMR)

AF:

0.330

AC:

5033

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.230

AC:

796

AN:

3468

East Asian (EAS)

AF:

0.430

AC:

2216

AN:

5156

South Asian (SAS)

AF:

0.239

AC:

1150

AN:

4818

European-Finnish (FIN)

AF:

0.331

AC:

3495

AN:

10554

Middle Eastern (MID)

AF:

0.177

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.388

AC:

26389

AN:

67936

Other (OTH)

AF:

0.293

AC:

617

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1646

3291

4937

6582

8228

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

488

976

1464

1952

2440

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.366

Hom.:

18251

Bravo

AF:

0.319

Asia WGS

AF:

0.321

AC:

1119

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

0.35

(source)

DANN

Benign

0.34

PhyloP100

-0.33

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over