chr2-206445446-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_003812.4(ADAM23):āc.354A>Gā(p.Ile118Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00262 in 1,614,192 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I118T) has been classified as Uncertain significance.
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.354A>G | p.Ile118Met | missense_variant | 2/26 | ENST00000264377.8 | |
ADAM23 | NM_001410985.1 | c.354A>G | p.Ile118Met | missense_variant | 2/26 | ||
ADAM23 | XM_005246932.4 | c.354A>G | p.Ile118Met | missense_variant | 2/25 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAM23 | ENST00000264377.8 | c.354A>G | p.Ile118Met | missense_variant | 2/26 | 1 | NM_003812.4 | P4 | |
ADAM23 | ENST00000374415.7 | c.354A>G | p.Ile118Met | missense_variant | 2/26 | 5 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00177 AC: 270AN: 152238Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00204 AC: 513AN: 251360Hom.: 1 AF XY: 0.00208 AC XY: 283AN XY: 135856
GnomAD4 exome AF: 0.00271 AC: 3962AN: 1461836Hom.: 10 Cov.: 31 AF XY: 0.00272 AC XY: 1977AN XY: 727218
GnomAD4 genome AF: 0.00177 AC: 270AN: 152356Hom.: 0 Cov.: 32 AF XY: 0.00154 AC XY: 115AN XY: 74500
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 06, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at