rs11065202

Positions:

• chr12-120674626-T-C

Variant summary

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

The XM_017020235.2(CABP1):​c.1088-5682T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 152,032 control chromosomes in the GnomAD database, including 18,243 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 0.48 (18243 hom., cov: 32)
• Consequence: CABP1 XM_017020235.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.95

Genes affected

CABP1 (HGNC:1384): (calcium binding protein 1) Calcium binding proteins are an important component of calcium mediated cellular signal transduction. This gene encodes a protein that belongs to a subfamily of calcium binding proteins which share similarity to calmodulin. The protein encoded by this gene regulates the gating of voltage-gated calcium ion channels. This protein inhibits calcium-dependent inactivation and supports calcium-dependent facilitation of ion channels containing voltage-dependent L-type calcium channel subunit alpha-1C. This protein also regulates calcium-dependent activity of inositol 1,4,5-triphosphate receptors, P/Q-type voltage-gated calcium channels, and transient receptor potential channel TRPC5. This gene is predominantly expressed in retina and brain. Alternative splicing results in multiple transcript variants encoding disinct isoforms. [provided by RefSeq, Jul 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CABP1	XM_017020235.2	c.1088-5682T>C		intron_variant			XP_016875724.1
CABP1	XM_024449280.2	c.896-5682T>C		intron_variant			XP_024305048.1
CABP1	XM_017020238.3	c.659-5682T>C		intron_variant			XP_016875727.1
CABP1	XM_017020239.3	c.479-5682T>C		intron_variant			XP_016875728.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73029 AN: 151914 Hom.: 18218 Cov.: 32

Gnomad AFR AF: 0.600

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.481 AC: 73105 AN: 152032 Hom.: 18243 Cov.: 32 AF XY: 0.487 AC XY: 36217 AN XY: 74320

Gnomad4 AFR AF: 0.601

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.372

Gnomad4 SAS AF: 0.566

Gnomad4 FIN AF: 0.436

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.504

Alfa AF: 0.428 Hom.: 15019

Bravo AF: 0.490

Asia WGS AF: 0.509 AC: 1770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11065202; hg19: chr12-121112429;