dbSNP rs9645664: CENATAC:c.383+4168T>C (chr11-119003277-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_198489.3(CENATAC):c.383+4168T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 526,796 control chromosomes in the GnomAD database, including 17,778 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 0.27 ( 5782 hom., cov: 31)

Exomes 𝑓: 0.24 ( 11996 hom. )

Consequence

CENATAC
NM_198489.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.183

Publications

13 publications found

Variant links:

Genes affected

CENATAC (HGNC:30460): (centrosomal AT-AC splicing factor) This gene encodes a protein thought to contain a coiled coil motif. No function has been determined for the encoded protein. A pseudogene of this gene is located on chromosome 20. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

CENATAC links:

RPL23AP64 (HGNC:36552): (ribosomal protein L23a pseudogene 64)

RPL23AP64 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=-0.64).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CENATAC	NM_198489.3 link	c.383+4168T>C		intron_variant	Intron 3 of 10	ENST00000334418.6	NP_940891.1	Q86UT8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CENATAC	ENST00000334418.6 link	c.383+4168T>C		intron_variant	Intron 3 of 10	1	NM_198489.3	ENSP00000334767.1		Q86UT8

Frequencies

GnomAD3 genomes

AF:

0.267

AC:

40587

AN:

151976

Hom.:

5764

Cov.:

show subpopulations

Gnomad AFR

AF:

0.342

Gnomad AMI

AF:

0.181

Gnomad AMR

AF:

0.219

Gnomad ASJ

AF:

0.185

Gnomad EAS

AF:

0.0731

Gnomad SAS

AF:

0.309

Gnomad FIN

AF:

0.273

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.249

Gnomad OTH

AF:

0.261

GnomAD4 exome

AF:

0.243

AC:

91004

AN:

374702

Hom.:

11996

Cov.:

AF XY:

0.249

AC XY:

53552

AN XY:

214770

show subpopulations

African (AFR)

AF:

0.344

AC:

3551

AN:

10326

American (AMR)

AF:

0.160

AC:

5579

AN:

34898

Ashkenazi Jewish (ASJ)

AF:

0.197

AC:

2323

AN:

11768

East Asian (EAS)

AF:

0.0721

AC:

1075

AN:

14920

South Asian (SAS)

AF:

0.294

AC:

19638

AN:

66752

European-Finnish (FIN)

AF:

0.263

AC:

4517

AN:

17186

Middle Eastern (MID)

AF:

0.246

AC:

357

AN:

1452

European-Non Finnish (NFE)

AF:

0.248

AC:

49584

AN:

200074

Other (OTH)

AF:

0.253

AC:

4380

AN:

17326

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

3571

7141

10712

14282

17853

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

380

760

1140

1520

1900

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.267

AC:

40646

AN:

152094

Hom.:

5782

Cov.:

AF XY:

0.265

AC XY:

19706

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.342

AC:

14184

AN:

41476

American (AMR)

AF:

0.219

AC:

3339

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.185

AC:

642

AN:

3466

East Asian (EAS)

AF:

0.0733

AC:

379

AN:

5170

South Asian (SAS)

AF:

0.309

AC:

1491

AN:

4824

European-Finnish (FIN)

AF:

0.273

AC:

2889

AN:

10572

Middle Eastern (MID)

AF:

0.337

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.249

AC:

16902

AN:

67996

Other (OTH)

AF:

0.264

AC:

557

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1504

3008

4513

6017

7521

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

412

824

1236

1648

2060

<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:

0.245

Hom.:

750

Bravo

AF:

0.263

Asia WGS

AF:

0.227

AC:

793

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

4.6

(source)

DANN

Benign

0.58

PhyloP100

0.18

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over