Genetic Variant CLIP4:c.1534+41G>A (chr2-29160508-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 NM_024692.6(CLIP4):c.1534+41G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.899 in 1,605,518 control chromosomes in the GnomAD database, including 650,446 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 0.88 ( 59630 hom., cov: 32)

Exomes 𝑓: 0.90 ( 590816 hom. )

Consequence

CLIP4
NM_024692.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.102

Publications

9 publications found

Variant links:

Genes affected

CLIP4 (HGNC:26108): (CAP-Gly domain containing linker protein family member 4) Predicted to enable microtubule plus-end binding activity. Predicted to be involved in cytoplasmic microtubule organization. Located in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

CLIP4 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=-0.94).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLIP4	NM_024692.6 link	c.1534+41G>A		intron_variant	Intron 12 of 15	ENST00000320081.10	NP_078968.3	Q8N3C7-1B7Z936

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLIP4	ENST00000320081.10 link	c.1534+41G>A		intron_variant	Intron 12 of 15	1	NM_024692.6	ENSP00000327009.5		Q8N3C7-1

Frequencies

GnomAD3 genomes

AF:

0.884

AC:

134475

AN:

152128

Hom.:

59578

Cov.:

show subpopulations

Gnomad AFR

AF:

0.827

Gnomad AMI

AF:

0.838

Gnomad AMR

AF:

0.909

Gnomad ASJ

AF:

0.878

Gnomad EAS

AF:

0.868

Gnomad SAS

AF:

0.837

Gnomad FIN

AF:

0.931

Gnomad MID

AF:

0.826

Gnomad NFE

AF:

0.912

Gnomad OTH

AF:

0.880

GnomAD2 exomes

AF:

0.896

AC:

220732

AN:

246486

AF XY:

0.892

show subpopulations

Gnomad AFR exome

AF:

0.828

Gnomad AMR exome

AF:

0.940

Gnomad ASJ exome

AF:

0.884

Gnomad EAS exome

AF:

0.870

Gnomad FIN exome

AF:

0.930

Gnomad NFE exome

AF:

0.909

Gnomad OTH exome

AF:

0.897

GnomAD4 exome

AF:

0.901

AC:

1309472

AN:

1453272

Hom.:

590816

Cov.:

AF XY:

0.899

AC XY:

649166

AN XY:

722252

show subpopulations

African (AFR)

AF:

0.827

AC:

27366

AN:

33098

American (AMR)

AF:

0.937

AC:

40928

AN:

43678

Ashkenazi Jewish (ASJ)

AF:

0.884

AC:

22791

AN:

25780

East Asian (EAS)

AF:

0.842

AC:

33332

AN:

39576

South Asian (SAS)

AF:

0.826

AC:

69952

AN:

84658

European-Finnish (FIN)

AF:

0.927

AC:

49438

AN:

53306

Middle Eastern (MID)

AF:

0.834

AC:

4757

AN:

5706

European-Non Finnish (NFE)

AF:

0.910

AC:

1007664

AN:

1107466

Other (OTH)

AF:

0.887

AC:

53244

AN:

60004

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.467

Heterozygous variant carriers

5519

11038

16557

22076

27595

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

21422

42844

64266

85688

107110

<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:

0.884

AC:

134584

AN:

152246

Hom.:

59630

Cov.:

AF XY:

0.885

AC XY:

65860

AN XY:

74438

show subpopulations

African (AFR)

AF:

0.827

AC:

34321

AN:

41500

American (AMR)

AF:

0.909

AC:

13906

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.878

AC:

3046

AN:

3470

East Asian (EAS)

AF:

0.868

AC:

4500

AN:

5184

South Asian (SAS)

AF:

0.836

AC:

4033

AN:

4826

European-Finnish (FIN)

AF:

0.931

AC:

9882

AN:

10610

Middle Eastern (MID)

AF:

0.823

AC:

242

AN:

294

European-Non Finnish (NFE)

AF:

0.912

AC:

62029

AN:

68038

Other (OTH)

AF:

0.881

AC:

1861

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

808

1616

2423

3231

4039

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

902

1804

2706

3608

4510

<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:

0.899

Hom.:

50851

Bravo

AF:

0.879

Asia WGS

AF:

0.867

AC:

3016

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.24

(source)

DANN

Benign

0.30

PhyloP100

-0.10

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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