21-25698706-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PM1PM2BP4_Strong
The NM_021219.4(JAM2):c.424C>A(p.Pro142Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00016 in 1,613,898 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar 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 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
JAM2 | ENST00000480456.6 | c.424C>A | p.Pro142Thr | missense_variant | Exon 5 of 10 | 1 | NM_021219.4 | ENSP00000420419.1 | ||
JAM2 | ENST00000400532.5 | c.424C>A | p.Pro142Thr | missense_variant | Exon 5 of 10 | 1 | ENSP00000383376.1 | |||
JAM2 | ENST00000312957.9 | c.316C>A | p.Pro106Thr | missense_variant | Exon 4 of 9 | 2 | ENSP00000318416.6 | |||
JAM2 | ENST00000460679.5 | n.289C>A | non_coding_transcript_exon_variant | Exon 3 of 9 | 3 | ENSP00000436801.1 |
Frequencies
GnomAD3 genomes AF: 0.000177 AC: 27AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000261 AC: 65AN: 249394Hom.: 0 AF XY: 0.000288 AC XY: 39AN XY: 135308
GnomAD4 exome AF: 0.000158 AC: 231AN: 1461764Hom.: 0 Cov.: 31 AF XY: 0.000171 AC XY: 124AN XY: 727174
GnomAD4 genome AF: 0.000177 AC: 27AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74332
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.424C>A (p.P142T) alteration is located in exon 5 (coding exon 5) of the JAM2 gene. This alteration results from a C to A substitution at nucleotide position 424, causing the proline (P) at amino acid position 142 to be replaced by a threonine (T). 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