dbSNP rs17501521: CABP4:c.542-56C>T (chr11-67457517-C-T) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_145200.5(CABP4):c.542-56C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 1,467,236 control chromosomes in the GnomAD database, including 81,411 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.25 ( 5719 hom., cov: 32)

Exomes 𝑓: 0.33 ( 75692 hom. )

Consequence

CABP4
NM_145200.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.459

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

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

BP6

Variant 11-67457517-C-T is Benign according to our data. Variant chr11-67457517-C-T is described in ClinVar as [Benign]. Clinvar id is 1247835.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CABP4	NM_145200.5 link	c.542-56C>T		intron_variant	Intron 3 of 5	ENST00000325656.7	NP_660201.1	P57796-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CABP4	ENST00000325656.7 link	c.542-56C>T	intron_variant	Intron 3 of 5	1	NM_145200.5	ENSP00000324960.5	P57796-1
CABP4	ENST00000438189.6 link	c.227-56C>T	intron_variant	Intron 4 of 6	1		ENSP00000401555.2	P57796-2
CABP4	ENST00000545777.1 link	n.*198-56C>T	intron_variant	Intron 3 of 3	3		ENSP00000439145.1	F5H3E8

Frequencies

GnomAD3 genomes

AF:

0.255

AC:

38766

AN:

151896

Hom.:

5722

Cov.:

show subpopulations

Gnomad AFR

AF:

0.137

Gnomad AMI

AF:

0.318

Gnomad AMR

AF:

0.207

Gnomad ASJ

AF:

0.223

Gnomad EAS

AF:

0.0844

Gnomad SAS

AF:

0.192

Gnomad FIN

AF:

0.264

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.355

Gnomad OTH

AF:

0.258

GnomAD4 exome

AF:

0.329

AC:

433108

AN:

1315222

Hom.:

75692

AF XY:

0.326

AC XY:

212905

AN XY:

653104

show subpopulations

Gnomad4 AFR exome

AF:

0.133

Gnomad4 AMR exome

AF:

0.176

Gnomad4 ASJ exome

AF:

0.223

Gnomad4 EAS exome

AF:

0.0880

Gnomad4 SAS exome

AF:

0.208

Gnomad4 FIN exome

AF:

0.268

Gnomad4 NFE exome

AF:

0.366

Gnomad4 OTH exome

AF:

0.301

GnomAD4 genome

AF:

0.255

AC:

38759

AN:

152014

Hom.:

5719

Cov.:

AF XY:

0.247

AC XY:

18323

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.137

Gnomad4 AMR

AF:

0.206

Gnomad4 ASJ

AF:

0.223

Gnomad4 EAS

AF:

0.0840

Gnomad4 SAS

AF:

0.192

Gnomad4 FIN

AF:

0.264

Gnomad4 NFE

AF:

0.355

Gnomad4 OTH

AF:

0.256

Alfa

AF:

0.311

Hom.:

5532

Bravo

AF:

0.246

Asia WGS

AF:

0.170

AC:

594

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Mar 03, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.22

DANN

Benign

0.61

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over