chr21-25639842-C-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_021219.4(JAM2):c.21C>A(p.His7Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00317 in 1,590,384 control chromosomes in the GnomAD database, including 125 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_021219.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
JAM2 | NM_021219.4 | c.21C>A | p.His7Gln | missense_variant | Exon 1 of 10 | ENST00000480456.6 | NP_067042.1 | |
JAM2 | NM_001270408.2 | c.21C>A | p.His7Gln | missense_variant | Exon 1 of 10 | NP_001257337.1 | ||
JAM2 | NM_001270407.2 | c.21C>A | p.His7Gln | missense_variant | Exon 1 of 9 | NP_001257336.1 | ||
JAM2 | NR_072999.2 | n.585C>A | non_coding_transcript_exon_variant | Exon 1 of 10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
JAM2 | ENST00000480456.6 | c.21C>A | p.His7Gln | missense_variant | Exon 1 of 10 | 1 | NM_021219.4 | ENSP00000420419.1 | ||
JAM2 | ENST00000400532.5 | c.21C>A | p.His7Gln | missense_variant | Exon 1 of 10 | 1 | ENSP00000383376.1 | |||
JAM2 | ENST00000312957.9 | c.21C>A | p.His7Gln | missense_variant | Exon 1 of 9 | 2 | ENSP00000318416.6 |
Frequencies
GnomAD3 genomes AF: 0.0170 AC: 2578AN: 151890Hom.: 66 Cov.: 32
GnomAD3 exomes AF: 0.00385 AC: 800AN: 207972Hom.: 21 AF XY: 0.00293 AC XY: 331AN XY: 113000
GnomAD4 exome AF: 0.00171 AC: 2453AN: 1438374Hom.: 59 Cov.: 30 AF XY: 0.00142 AC XY: 1010AN XY: 713582
GnomAD4 genome AF: 0.0170 AC: 2581AN: 152010Hom.: 66 Cov.: 32 AF XY: 0.0160 AC XY: 1189AN XY: 74318
ClinVar
Submissions by phenotype
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at