Variant 19-48040605-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_019855.5(CABP5):c.238C>T(p.Leu80Leu) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.816 in 1,613,232 control chromosomes in the GnomAD database, including 538,615 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.79 ( 47503 hom., cov: 30)

Exomes 𝑓: 0.82 ( 491112 hom. )

Consequence

CABP5
NM_019855.5 splice_region, synonymous

Scores

Splicing: ADA: 0.0001021

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.632

Variant links:

Genes affected

CABP5 (HGNC:13714): (calcium binding protein 5) The product of this gene belongs to a subfamily of calcium binding proteins, which share similarity to calmodulin. Calcium binding proteins are an important component of calcium mediated cellular signal transduction. Expression of this gene is retina-specific. The mouse homolog of this protein has been shown to express in the inner nuclear layer of the retina, suggested its role in neuronal functioning. The specific function of this gene is unknown. [provided by RefSeq, Oct 2009]

CABP5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.34).

BP7

Synonymous conserved (PhyloP=-0.632 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CABP5	NM_019855.5 linkuse as main transcript	c.238C>T	p.Leu80Leu	splice_region_variant, synonymous_variant	3/6	ENST00000293255.3	NP_062829.1	Q9NP86

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CABP5	ENST00000293255.3 linkuse as main transcript	c.238C>T	p.Leu80Leu	splice_region_variant, synonymous_variant	3/6	1	NM_019855.5	ENSP00000293255.1		Q9NP86

Frequencies

GnomAD3 genomes

AF:

0.787

AC:

119538

AN:

151866

Hom.:

47485

Cov.:

show subpopulations

Gnomad AFR

AF:

0.679

Gnomad AMI

AF:

0.936

Gnomad AMR

AF:

0.834

Gnomad ASJ

AF:

0.741

Gnomad EAS

AF:

0.855

Gnomad SAS

AF:

0.814

Gnomad FIN

AF:

0.864

Gnomad MID

AF:

0.845

Gnomad NFE

AF:

0.823

Gnomad OTH

AF:

0.810

GnomAD3 exomes

AF:

0.816

AC:

204933

AN:

251050

Hom.:

83966

AF XY:

0.818

AC XY:

110971

AN XY:

135686

show subpopulations

Gnomad AFR exome

AF:

0.672

Gnomad AMR exome

AF:

0.834

Gnomad ASJ exome

AF:

0.759

Gnomad EAS exome

AF:

0.863

Gnomad SAS exome

AF:

0.812

Gnomad FIN exome

AF:

0.863

Gnomad NFE exome

AF:

0.821

Gnomad OTH exome

AF:

0.825

GnomAD4 exome

AF:

0.819

AC:

1197083

AN:

1461248

Hom.:

491112

Cov.:

AF XY:

0.819

AC XY:

595534

AN XY:

726946

show subpopulations

Gnomad4 AFR exome

AF:

0.677

Gnomad4 AMR exome

AF:

0.835

Gnomad4 ASJ exome

AF:

0.757

Gnomad4 EAS exome

AF:

0.835

Gnomad4 SAS exome

AF:

0.807

Gnomad4 FIN exome

AF:

0.858

Gnomad4 NFE exome

AF:

0.823

Gnomad4 OTH exome

AF:

0.817

GnomAD4 genome

AF:

0.787

AC:

119601

AN:

151984

Hom.:

47503

Cov.:

AF XY:

0.791

AC XY:

58760

AN XY:

74276

show subpopulations

Gnomad4 AFR

AF:

0.678

Gnomad4 AMR

AF:

0.834

Gnomad4 ASJ

AF:

0.741

Gnomad4 EAS

AF:

0.855

Gnomad4 SAS

AF:

0.813

Gnomad4 FIN

AF:

0.864

Gnomad4 NFE

AF:

0.823

Gnomad4 OTH

AF:

0.809

Alfa

AF:

0.816

Hom.:

123714

Bravo

AF:

0.782

Asia WGS

AF:

0.839

AC:

2920

AN:

3478

EpiCase

AF:

0.822

EpiControl

AF:

0.826

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.34

CADD

Benign

1.9

DANN

Benign

0.65

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00010

dbscSNV1_RF

Benign

0.0

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over