ENST00000765072.1:n.329-4876A>G

Variant names:

• chr12-120674626-T-C
• rs11065202
• ENST00000765072.1:n.329-4876A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000765072.1(ENSG00000299604):​n.329-4876A>G 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: ENSG00000299604 ENST00000765072.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.95
• Publications: 20 publications found

Genes affected

ENSG00000299604 (HGNC:):

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CABP1	XM_017020235.2	c.1088-5682T>C		intron_variant	Intron 5 of 5		XP_016875724.1
CABP1	XM_024449280.2	c.896-5682T>C		intron_variant	Intron 5 of 5		XP_024305048.1
CABP1	XM_017020238.3	c.659-5682T>C		intron_variant	Intron 6 of 6		XP_016875727.1
CABP1	XM_017020239.3	c.479-5682T>C		intron_variant	Intron 5 of 5		XP_016875728.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299604	ENST00000765072.1	n.329-4876A>G		intron_variant	Intron 3 of 3

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

African (AFR) AF: 0.601 AC: 24899 AN: 41462

American (AMR) AF: 0.522 AC: 7971 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1405 AN: 3470

East Asian (EAS) AF: 0.372 AC: 1923 AN: 5164

South Asian (SAS) AF: 0.566 AC: 2732 AN: 4828

European-Finnish (FIN) AF: 0.436 AC: 4610 AN: 10568

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 27970 AN: 67958

Other (OTH) AF: 0.504 AC: 1065 AN: 2112

Alfa AF: 0.433 Hom.: 20625

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
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs11065202; hg19: chr12-121112429;