21-25689968-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM1PM2
The NM_021219.4(JAM2):c.236T>C(p.Leu79Pro) variant causes a missense change. The variant allele was found at a frequency of 0.0000269 in 1,596,182 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L79F) has been classified as Uncertain significance.
Frequency
Consequence
NM_021219.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
JAM2 | NM_021219.4 | c.236T>C | p.Leu79Pro | missense_variant | Exon 3 of 10 | ENST00000480456.6 | NP_067042.1 | |
JAM2 | NM_001270408.2 | c.236T>C | p.Leu79Pro | missense_variant | Exon 3 of 10 | NP_001257337.1 | ||
JAM2 | NM_001270407.2 | c.134-3788T>C | intron_variant | Intron 2 of 8 | NP_001257336.1 | |||
JAM2 | NR_072999.2 | n.800T>C | non_coding_transcript_exon_variant | Exon 3 of 10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
JAM2 | ENST00000480456.6 | c.236T>C | p.Leu79Pro | missense_variant | Exon 3 of 10 | 1 | NM_021219.4 | ENSP00000420419.1 | ||
JAM2 | ENST00000400532.5 | c.236T>C | p.Leu79Pro | missense_variant | Exon 3 of 10 | 1 | ENSP00000383376.1 | |||
JAM2 | ENST00000312957.9 | c.134-3788T>C | intron_variant | Intron 2 of 8 | 2 | ENSP00000318416.6 | ||||
JAM2 | ENST00000460679.5 | n.101T>C | non_coding_transcript_exon_variant | Exon 1 of 9 | 3 | ENSP00000436801.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000804 AC: 2AN: 248836Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135112
GnomAD4 exome AF: 0.0000291 AC: 42AN: 1443964Hom.: 0 Cov.: 25 AF XY: 0.0000278 AC XY: 20AN XY: 719494
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152218Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74364
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.236T>C (p.L79P) alteration is located in exon 3 (coding exon 3) of the JAM2 gene. This alteration results from a T to C substitution at nucleotide position 236, causing the leucine (L) at amino acid position 79 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at