Genetic Variant NM_024692.6: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

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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