11-67456449-CA-GT

Variant names:

• chr11-67456449-CA-GT
• rs34039523
• NM_145200.5:c.541+7_541+8delCAinsGT

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_145200.5(CABP4):​c.541+7_541+8delCAinsGT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 31)
• Consequence: CABP4 NM_145200.5 splice_region, intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.829
• Publications: 0 publications found

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: G2P, Labcorp Genetics (formerly Invitae)
• autosomal dominant nocturnal frontal lobe epilepsy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• congenital stationary night blindness

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• BP6: Variant 11-67456449-CA-GT is Benign according to our data. Variant chr11-67456449-CA-GT is described in CliVar as Likely_benign. Clinvar id is 1111850.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-67456449-CA-GT is described in CliVar as Likely_benign. Clinvar id is 1111850.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-67456449-CA-GT is described in CliVar as Likely_benign. Clinvar id is 1111850.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-67456449-CA-GT is described in CliVar as Likely_benign. Clinvar id is 1111850.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-67456449-CA-GT is described in CliVar as Likely_benign. Clinvar id is 1111850.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-67456449-CA-GT is described in CliVar as Likely_benign. Clinvar id is 1111850.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CABP4	NM_145200.5	c.541+7_541+8delCAinsGT		splice_region_variant, intron_variant	Intron 3 of 5	ENST00000325656.7	NP_660201.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CABP4	ENST00000325656.7	c.541+7_541+8delCAinsGT		splice_region_variant, intron_variant	Intron 3 of 5	1	NM_145200.5	ENSP00000324960.5
CABP4	ENST00000438189.6	c.226+7_226+8delCAinsGT		splice_region_variant, intron_variant	Intron 4 of 6	1		ENSP00000401555.2
CABP4	ENST00000545777.1	n.*197+32_*197+33delCAinsGT		intron_variant	Intron 3 of 3	3		ENSP00000439145.1

Frequencies

GnomAD3 genomes Cov.: 31

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 31

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Dec 16, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs34039523; hg19: chr11-67223920;