Genetic Variant CIBAR2:c.433-136C>A (chr16-85105567-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_198491.3(CIBAR2):c.433-136C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 636,618 control chromosomes in the GnomAD database, including 110,610 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 0.64 ( 32414 hom., cov: 32)

Exomes 𝑓: 0.56 ( 78196 hom. )

Consequence

CIBAR2
NM_198491.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.19

Publications

19 publications found

Variant links:

Genes affected

CIBAR2 (HGNC:24781): (CBY1 interacting BAR domain containing 2) Predicted to be involved in cilium assembly. Predicted to be located in centriole and cytoplasm. Predicted to be active in ciliary basal body and ciliary transition zone. [provided by Alliance of Genome Resources, Apr 2022]

CIBAR2 links:

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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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198491.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CIBAR2	NM_198491.3	MANE Select	c.433-136C>A		intron	N/A	NP_940893.1
	CIBAR2	NM_001366920.1		c.433-136C>A		intron	N/A	NP_001353849.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CIBAR2	ENST00000539556.6	TSL:5 MANE Select	c.433-136C>A		intron	N/A	ENSP00000443411.1
	CIBAR2	ENST00000618669.3	TSL:5	c.148-136C>A		intron	N/A	ENSP00000478373.1

Frequencies

GnomAD3 genomes

AF:

0.636

AC:

96609

AN:

151970

Hom.:

32366

Cov.:

show subpopulations

Gnomad AFR

AF:

0.866

Gnomad AMI

AF:

0.620

Gnomad AMR

AF:

0.541

Gnomad ASJ

AF:

0.586

Gnomad EAS

AF:

0.337

Gnomad SAS

AF:

0.593

Gnomad FIN

AF:

0.469

Gnomad MID

AF:

0.666

Gnomad NFE

AF:

0.571

Gnomad OTH

AF:

0.642

GnomAD4 exome

AF:

0.558

AC:

270406

AN:

484530

Hom.:

78196

AF XY:

0.562

AC XY:

142792

AN XY:

254214

show subpopulations

African (AFR)

AF:

0.863

AC:

11892

AN:

13786

American (AMR)

AF:

0.495

AC:

10958

AN:

22152

Ashkenazi Jewish (ASJ)

AF:

0.589

AC:

8389

AN:

14232

East Asian (EAS)

AF:

0.321

AC:

9966

AN:

31086

South Asian (SAS)

AF:

0.609

AC:

28861

AN:

47364

European-Finnish (FIN)

AF:

0.483

AC:

15026

AN:

31098

Middle Eastern (MID)

AF:

0.654

AC:

2359

AN:

3606

European-Non Finnish (NFE)

AF:

0.568

AC:

167173

AN:

294258

Other (OTH)

AF:

0.586

AC:

15782

AN:

26948

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

5485

10970

16454

21939

27424

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1448

2896

4344

5792

7240

<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:

0.636

AC:

96706

AN:

152088

Hom.:

32414

Cov.:

AF XY:

0.629

AC XY:

46728

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.866

AC:

35951

AN:

41518

American (AMR)

AF:

0.540

AC:

8254

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.586

AC:

2035

AN:

3472

East Asian (EAS)

AF:

0.338

AC:

1743

AN:

5164

South Asian (SAS)

AF:

0.593

AC:

2859

AN:

4820

European-Finnish (FIN)

AF:

0.469

AC:

4950

AN:

10564

Middle Eastern (MID)

AF:

0.671

AC:

196

AN:

292

European-Non Finnish (NFE)

AF:

0.571

AC:

38796

AN:

67964

Other (OTH)

AF:

0.644

AC:

1359

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1676

3353

5029

6706

8382

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

772

1544

2316

3088

3860

<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:

0.604

Hom.:

58557

Bravo

AF:

0.649

Asia WGS

AF:

0.504

AC:

1755

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.058

(source)

DANN

Benign

0.73

PhyloP100

-1.2

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over