rs17501521

chr11-67457517-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.459

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]

ACMG classification

Verdict is Benign. Variant got -14 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_single_submitter, 1 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/exons	MANE	UniProt
CABP4	NM_145200.5	c.542-56C>T		intron_variant		ENST00000325656.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CABP4	ENST00000325656.7	c.542-56C>T		intron_variant		1	NM_145200.5	P1
CABP4	ENST00000438189.6	c.227-56C>T		intron_variant		1
CABP4	ENST00000545777.1	c.*198-56C>T		intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38766 AN: 151896 Hom.: 5722 Cov.: 32

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

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.: 32 AF XY: 0.247 AC XY: 18323 AN XY: 74314

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:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 03, 2015

- -

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

Other links and lift over

dbSNP: rs17501521; hg19: chr11-67224988; COSMIC: COSV56886794; COSMIC: COSV56886794;