Genetic Variant NM_198559.2:c.54G>A (chr2-218357123-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_198559.2(CATIP):c.54G>A(p.Ser18Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 1,612,536 control chromosomes in the GnomAD database, including 35,654 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 0.17 ( 2549 hom., cov: 30)

Exomes 𝑓: 0.21 ( 33105 hom. )

Consequence

CATIP
NM_198559.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.61

Publications

19 publications found

Variant links:

Genes affected

CATIP (HGNC:25062): (ciliogenesis associated TTC17 interacting protein) Involved in actin filament polymerization and cilium organization. Located in several cellular components, including actin cytoskeleton; nucleus; and plasma membrane. Implicated in spermatogenic failure. [provided by Alliance of Genome Resources, Apr 2022]

CATIP links:

CATIP-AS2 (HGNC:41079): (CATIP antisense RNA 2)

CATIP-AS2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP7

Synonymous conserved (PhyloP=-1.61 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CATIP	NM_198559.2 link	c.54G>A	p.Ser18Ser	synonymous_variant	Exon 2 of 10	ENST00000289388.4	NP_940961.1	Q7Z7H3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CATIP	ENST00000289388.4 link	c.54G>A	p.Ser18Ser	synonymous_variant	Exon 2 of 10	1	NM_198559.2	ENSP00000289388.3		Q7Z7H3

Frequencies

GnomAD3 genomes

AF:

0.167

AC:

25344

AN:

151846

Hom.:

2546

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0625

Gnomad AMI

AF:

0.268

Gnomad AMR

AF:

0.256

Gnomad ASJ

AF:

0.221

Gnomad EAS

AF:

0.122

Gnomad SAS

AF:

0.0674

Gnomad FIN

AF:

0.152

Gnomad MID

AF:

0.320

Gnomad NFE

AF:

0.217

Gnomad OTH

AF:

0.210

GnomAD2 exomes

AF:

0.187

AC:

46893

AN:

250848

AF XY:

0.182

show subpopulations

Gnomad AFR exome

AF:

0.0608

Gnomad AMR exome

AF:

0.284

Gnomad ASJ exome

AF:

0.219

Gnomad EAS exome

AF:

0.119

Gnomad FIN exome

AF:

0.164

Gnomad NFE exome

AF:

0.219

Gnomad OTH exome

AF:

0.226

GnomAD4 exome

AF:

0.206

AC:

301238

AN:

1460572

Hom.:

33105

Cov.:

AF XY:

0.202

AC XY:

147046

AN XY:

726652

show subpopulations

African (AFR)

AF:

0.0547

AC:

1831

AN:

33466

American (AMR)

AF:

0.284

AC:

12673

AN:

44642

Ashkenazi Jewish (ASJ)

AF:

0.219

AC:

5725

AN:

26098

East Asian (EAS)

AF:

0.137

AC:

5456

AN:

39698

South Asian (SAS)

AF:

0.0671

AC:

5788

AN:

86218

European-Finnish (FIN)

AF:

0.163

AC:

8705

AN:

53406

Middle Eastern (MID)

AF:

0.230

AC:

1326

AN:

5768

European-Non Finnish (NFE)

AF:

0.223

AC:

247732

AN:

1110924

Other (OTH)

AF:

0.199

AC:

12002

AN:

60352

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.463

Heterozygous variant carriers

11047

22095

33142

44190

55237

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8424

16848

25272

33696

42120

<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:

0.167

AC:

25357

AN:

151964

Hom.:

2549

Cov.:

AF XY:

0.165

AC XY:

12231

AN XY:

74260

show subpopulations

African (AFR)

AF:

0.0623

AC:

2585

AN:

41476

American (AMR)

AF:

0.257

AC:

3911

AN:

15242

Ashkenazi Jewish (ASJ)

AF:

0.221

AC:

765

AN:

3468

East Asian (EAS)

AF:

0.122

AC:

629

AN:

5154

South Asian (SAS)

AF:

0.0673

AC:

323

AN:

4802

European-Finnish (FIN)

AF:

0.152

AC:

1602

AN:

10544

Middle Eastern (MID)

AF:

0.316

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.217

AC:

14759

AN:

67960

Other (OTH)

AF:

0.211

AC:

446

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1025

2050

3074

4099

5124

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

268

536

804

1072

1340

<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:

0.209

Hom.:

6230

Bravo

AF:

0.176

Asia WGS

AF:

0.0780

AC:

272

AN:

3478

EpiCase

AF:

0.222

EpiControl

AF:

0.228

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

3.2

(source)

DANN

Benign

0.56

PhyloP100

-1.6

PromoterAI

-0.0036

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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