chr2-206445411-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_003812.4(ADAM23):c.319A>G(p.Met107Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00142 in 1,614,160 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_003812.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADAM23 | NM_003812.4 | c.319A>G | p.Met107Val | missense_variant | 2/26 | ENST00000264377.8 | |
ADAM23 | NM_001410985.1 | c.319A>G | p.Met107Val | missense_variant | 2/26 | ||
ADAM23 | XM_005246932.4 | c.319A>G | p.Met107Val | missense_variant | 2/25 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAM23 | ENST00000264377.8 | c.319A>G | p.Met107Val | missense_variant | 2/26 | 1 | NM_003812.4 | P4 | |
ADAM23 | ENST00000374415.7 | c.319A>G | p.Met107Val | missense_variant | 2/26 | 5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000828 AC: 126AN: 152226Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00130 AC: 328AN: 251450Hom.: 4 AF XY: 0.00149 AC XY: 203AN XY: 135898
GnomAD4 exome AF: 0.00148 AC: 2169AN: 1461816Hom.: 8 Cov.: 31 AF XY: 0.00152 AC XY: 1106AN XY: 727202
GnomAD4 genome ? AF: 0.000834 AC: 127AN: 152344Hom.: 0 Cov.: 32 AF XY: 0.000819 AC XY: 61AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at