Variant rs2829877 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The NM_021219.4(JAM2):c.*60T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.086 in 1,125,272 control chromosomes in the GnomAD database, including 4,556 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.093 ( 720 hom., cov: 32)

Exomes 𝑓: 0.085 ( 3836 hom. )

Consequence

JAM2
NM_021219.4 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.293

Variant links:

Genes affected

JAM2 (HGNC:14686): (junctional adhesion molecule 2) This gene belongs to the immunoglobulin superfamily, and the junctional adhesion molecule (JAM) family. The protein encoded by this gene is a type I membrane protein that is localized at the tight junctions of both epithelial and endothelial cells. It acts as an adhesive ligand for interacting with a variety of immune cell types, and may play a role in lymphocyte homing to secondary lymphoid organs. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2012]

JAM2 links:

LOC124905002 (HGNC:):

LOC124905002 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.28).

BP6

Variant 21-25714732-T-C is Benign according to our data. Variant chr21-25714732-T-C is described in ClinVar as [Benign]. Clinvar id is 1294897.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
JAM2	NM_021219.4 linkuse as main transcript	c.*60T>C	3_prime_UTR_variant	10/10	ENST00000480456.6
LOC124905002	XR_007067827.1 linkuse as main transcript	n.2841+2929A>G	intron_variant, non_coding_transcript_variant
JAM2	NM_001270407.2 linkuse as main transcript	c.*60T>C	3_prime_UTR_variant	9/9
JAM2	NR_072999.2 linkuse as main transcript	n.1517T>C	non_coding_transcript_exon_variant	10/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
JAM2	ENST00000480456.6 linkuse as main transcript	c.*60T>C		3_prime_UTR_variant	10/10	1	NM_021219.4	P1	P57087-1

Frequencies

GnomAD3 genomes

AF:

0.0927

AC:

14101

AN:

152056

Hom.:

713

Cov.:

show subpopulations

Gnomad AFR

AF:

0.115

Gnomad AMI

AF:

0.0143

Gnomad AMR

AF:

0.0802

Gnomad ASJ

AF:

0.0953

Gnomad EAS

AF:

0.0347

Gnomad SAS

AF:

0.0986

Gnomad FIN

AF:

0.0980

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.0857

Gnomad OTH

AF:

0.0872

GnomAD4 exome

AF:

0.0849

AC:

82618

AN:

973098

Hom.:

3836

Cov.:

AF XY:

0.0847

AC XY:

42016

AN XY:

495934

show subpopulations

Gnomad4 AFR exome

AF:

0.116

Gnomad4 AMR exome

AF:

0.0969

Gnomad4 ASJ exome

AF:

0.0931

Gnomad4 EAS exome

AF:

0.0248

Gnomad4 SAS exome

AF:

0.0916

Gnomad4 FIN exome

AF:

0.0954

Gnomad4 NFE exome

AF:

0.0846

Gnomad4 OTH exome

AF:

0.0843

GnomAD4 genome

AF:

0.0928

AC:

14128

AN:

152174

Hom.:

720

Cov.:

AF XY:

0.0946

AC XY:

7039

AN XY:

74414

show subpopulations

Gnomad4 AFR

AF:

0.115

Gnomad4 AMR

AF:

0.0800

Gnomad4 ASJ

AF:

0.0953

Gnomad4 EAS

AF:

0.0347

Gnomad4 SAS

AF:

0.0987

Gnomad4 FIN

AF:

0.0980

Gnomad4 NFE

AF:

0.0857

Gnomad4 OTH

AF:

0.0943

Alfa

AF:

0.0889

Hom.:

338

Bravo

AF:

0.0914

Asia WGS

AF:

0.0840

AC:

293

AN:

3470

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	clinical testing	GeneDx	May 13, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.28

CADD

Benign

DANN

Benign

0.74

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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