11-67454383-T-C

Position:

• chr11-67454383-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001300896.3(CABP4):​c.-112-1326T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 152,000 control chromosomes in the GnomAD database, including 23,285 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 0.52 (23285 hom., cov: 33)
• Consequence: CABP4 NM_001300896.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.668

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CABP4	XM_024448615.2	c.-1041T>C		5_prime_UTR_variant	2/7		XP_024304383.1
CABP4	NM_001300896.3	c.-112-1326T>C		intron_variant			NP_001287825.1
CABP4	NM_001379183.1	c.-387-1051T>C		intron_variant			NP_001366112.1
CABP4	XM_005274114.4	c.71-1051T>C		intron_variant			XP_005274171.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CABP4	ENST00000438189.6	c.-112-1326T>C		intron_variant		1		ENSP00000401555.2
CABP4	ENST00000538060.1	n.296-1051T>C		intron_variant		4
CABP4	ENST00000542025.2	n.408-1051T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79391 AN: 151882 Hom.: 23248 Cov.: 33

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.523 AC: 79475 AN: 152000 Hom.: 23285 Cov.: 33 AF XY: 0.512 AC XY: 38009 AN XY: 74290

Gnomad4 AFR AF: 0.808

Gnomad4 AMR AF: 0.503

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.469

Alfa AF: 0.479 Hom.: 2381

Bravo AF: 0.551

Asia WGS AF: 0.350 AC: 1219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.9
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1790761; hg19: chr11-67221854; COSMIC: COSV56888060; COSMIC: COSV56888060;