Variant 10-30026293-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_020848.4(JCAD):c.3855C>T(p.Ala1285Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00631 in 1,613,906 control chromosomes in the GnomAD database, including 48 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0044 ( 6 hom., cov: 32)

Exomes 𝑓: 0.0065 ( 42 hom. )

Consequence

JCAD
NM_020848.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -3.43

Variant links:

Genes affected

JCAD (HGNC:29283): (junctional cadherin 5 associated) This gene encodes an endothelial cell-to-cell junction protein. Naturally occurring mutations in this gene are associated with coronary artery disease, late onset alzheimer disease, and emphysema distribution. [provided by RefSeq, Mar 2017]

JCAD links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 10-30026293-G-A is Benign according to our data. Variant chr10-30026293-G-A is described in ClinVar as [Benign]. Clinvar id is 718174.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-3.43 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
JCAD	NM_020848.4 linkuse as main transcript	c.3855C>T	p.Ala1285Ala	synonymous_variant	3/4	ENST00000375377.2	NP_065899.1	Q9P266
JCAD	NM_001350022.2 linkuse as main transcript	c.3855C>T	p.Ala1285Ala	synonymous_variant	4/5		NP_001336951.1
JCAD	NM_001350001.2 linkuse as main transcript	c.3441C>T	p.Ala1147Ala	synonymous_variant	4/5		NP_001336930.1
JCAD	NM_001350021.2 linkuse as main transcript	c.3441C>T	p.Ala1147Ala	synonymous_variant	4/5		NP_001336950.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
JCAD	ENST00000375377.2 linkuse as main transcript	c.3855C>T	p.Ala1285Ala	synonymous_variant	3/4	5	NM_020848.4	ENSP00000364526.1		Q9P266

Frequencies

GnomAD3 genomes

AF:

0.00443

AC:

674

AN:

152168

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00145

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00347

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.000579

Gnomad SAS

AF:

0.000829

Gnomad FIN

AF:

0.00151

Gnomad MID

AF:

0.00318

Gnomad NFE

AF:

0.00773

Gnomad OTH

AF:

0.00478

GnomAD3 exomes

AF:

0.00416

AC:

1037

AN:

249096

Hom.:

AF XY:

0.00426

AC XY:

576

AN XY:

135184

show subpopulations

Gnomad AFR exome

AF:

0.00142

Gnomad AMR exome

AF:

0.00287

Gnomad ASJ exome

AF:

0.000497

Gnomad EAS exome

AF:

0.000111

Gnomad SAS exome

AF:

0.00127

Gnomad FIN exome

AF:

0.00164

Gnomad NFE exome

AF:

0.00717

Gnomad OTH exome

AF:

0.00396

GnomAD4 exome

AF:

0.00651

AC:

9508

AN:

1461620

Hom.:

Cov.:

AF XY:

0.00641

AC XY:

4664

AN XY:

727136

show subpopulations

Gnomad4 AFR exome

AF:

0.00116

Gnomad4 AMR exome

AF:

0.00279

Gnomad4 ASJ exome

AF:

0.000689

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00128

Gnomad4 FIN exome

AF:

0.00160

Gnomad4 NFE exome

AF:

0.00784

Gnomad4 OTH exome

AF:

0.00634

GnomAD4 genome

AF:

0.00441

AC:

672

AN:

152286

Hom.:

Cov.:

AF XY:

0.00414

AC XY:

308

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.00144

Gnomad4 AMR

AF:

0.00346

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.000387

Gnomad4 SAS

AF:

0.000830

Gnomad4 FIN

AF:

0.00151

Gnomad4 NFE

AF:

0.00773

Gnomad4 OTH

AF:

0.00473

Alfa

AF:

0.00570

Hom.:

Bravo

AF:

0.00473

Asia WGS

AF:

0.000866

AC:

AN:

3478

EpiCase

AF:

0.00802

EpiControl

AF:

0.00723

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jul 20, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.013

DANN

Benign

0.47

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over