rs72934713

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_145200.5(CABP4):c.800-5C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0781 in 1,613,978 control chromosomes in the GnomAD database, including 5,679 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.056 ( 339 hom., cov: 32)

Exomes 𝑓: 0.080 ( 5340 hom. )

Consequence

CABP4
NM_145200.5 splice_region, intron

Scores

Splicing: ADA: 0.00002486

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: -2.18

Publications

5 publications found

Variant links:

Genes affected

CABP4 (HGNC:1386): (calcium binding protein 4) This gene encodes a member of the CABP family of calcium binding protein characterized by four EF-hand motifs. Mutations in this gene are associated with congenital stationary night blindness type 2B. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jul 2014]

CABP4 Gene-Disease associations (from GenCC):

cone-rod synaptic disorder, congenital nonprogressive
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
autosomal dominant nocturnal frontal lobe epilepsy
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
congenital stationary night blindness
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

CABP4 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_145200.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 11-67458626-C-T is Benign according to our data. Variant chr11-67458626-C-T is described in ClinVar as Benign. ClinVar VariationId is 262580.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0875 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145200.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CABP4	NM_145200.5	MANE Select	c.800-5C>T	splice_region intron	N/A	NP_660201.1	P57796-1
CABP4	NM_001300895.3		c.485-5C>T	splice_region intron	N/A	NP_001287824.1	P57796-2
CABP4	NM_001300896.3		c.485-5C>T	splice_region intron	N/A	NP_001287825.1	P57796-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CABP4	ENST00000325656.7	TSL:1 MANE Select	c.800-5C>T		splice_region intron	N/A	ENSP00000324960.5	P57796-1
	CABP4	ENST00000438189.6	TSL:1	c.485-5C>T		splice_region intron	N/A	ENSP00000401555.2	P57796-2

Frequencies

GnomAD3 genomes

AF:

0.0560

AC:

8513

AN:

152110

Hom.:

340

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0173

Gnomad AMI

AF:

0.0482

Gnomad AMR

AF:

0.0398

Gnomad ASJ

AF:

0.0688

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.0539

Gnomad FIN

AF:

0.0398

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0894

Gnomad OTH

AF:

0.0565

GnomAD2 exomes

AF:

0.0589

AC:

14811

AN:

251300

AF XY:

0.0614

show subpopulations

Gnomad AFR exome

AF:

0.0176

Gnomad AMR exome

AF:

0.0274

Gnomad ASJ exome

AF:

0.0638

Gnomad EAS exome

AF:

0.000652

Gnomad FIN exome

AF:

0.0459

Gnomad NFE exome

AF:

0.0867

Gnomad OTH exome

AF:

0.0702

GnomAD4 exome

AF:

0.0805

AC:

117622

AN:

1461750

Hom.:

5340

Cov.:

AF XY:

0.0800

AC XY:

58202

AN XY:

727172

show subpopulations

African (AFR)

AF:

0.0141

AC:

472

AN:

33480

American (AMR)

AF:

0.0291

AC:

1301

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.0622

AC:

1625

AN:

26136

East Asian (EAS)

AF:

0.000227

AC:

AN:

39700

South Asian (SAS)

AF:

0.0541

AC:

4663

AN:

86258

European-Finnish (FIN)

AF:

0.0498

AC:

2654

AN:

53340

Middle Eastern (MID)

AF:

0.0923

AC:

532

AN:

5766

European-Non Finnish (NFE)

AF:

0.0917

AC:

101985

AN:

1111952

Other (OTH)

AF:

0.0725

AC:

4381

AN:

60394

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

6376

12752

19127

25503

31879

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3696

7392

11088

14784

18480

<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:

0.0559

AC:

8504

AN:

152228

Hom.:

339

Cov.:

AF XY:

0.0527

AC XY:

3924

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.0173

AC:

718

AN:

41560

American (AMR)

AF:

0.0396

AC:

606

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0688

AC:

239

AN:

3472

East Asian (EAS)

AF:

0.00135

AC:

AN:

5184

South Asian (SAS)

AF:

0.0533

AC:

257

AN:

4822

European-Finnish (FIN)

AF:

0.0398

AC:

422

AN:

10600

Middle Eastern (MID)

AF:

0.0612

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0894

AC:

6075

AN:

67982

Other (OTH)

AF:

0.0559

AC:

118

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

417

834

1252

1669

2086

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

196

294

392

490

<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:

0.0569

Hom.:

260

Bravo

AF:

0.0535

Asia WGS

AF:

0.0230

AC:

AN:

3478

EpiCase

AF:

0.0891

EpiControl

AF:

0.0846

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (3)

Cone-rod synaptic disorder, congenital nonprogressive (2)

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.10

(source)

DANN

Benign

0.56

PhyloP100

-2.2

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000025

dbscSNV1_RF

Benign

0.0060

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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