rs7284014
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_021219.4(JAM2):c.133+2129A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,120 control chromosomes in the GnomAD database, including 4,933 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 0.25 ( 4933 hom., cov: 32)
Consequence
JAM2
NM_021219.4 intron
NM_021219.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0400
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
JAM2 | NM_021219.4 | c.133+2129A>G | intron_variant | ENST00000480456.6 | |||
JAM2 | NM_001270407.2 | c.133+2129A>G | intron_variant | ||||
JAM2 | NM_001270408.2 | c.133+2129A>G | intron_variant | ||||
JAM2 | NR_072999.2 | n.697+2129A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JAM2 | ENST00000480456.6 | c.133+2129A>G | intron_variant | 1 | NM_021219.4 | P1 | |||
JAM2 | ENST00000400532.5 | c.133+2129A>G | intron_variant | 1 | |||||
JAM2 | ENST00000312957.9 | c.133+2129A>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.246 AC: 37434AN: 152002Hom.: 4924 Cov.: 32
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.246 AC: 37469AN: 152120Hom.: 4933 Cov.: 32 AF XY: 0.243 AC XY: 18086AN XY: 74368
GnomAD4 genome
?
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37469
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152120
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32
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18086
AN XY:
74368
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718
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at