chr2-213056961-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001387220.1(IKZF2):c.278A>G(p.Asn93Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0062 in 1,613,838 control chromosomes in the GnomAD database, including 63 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001387220.1 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IKZF2 | NM_001387220.1 | c.278A>G | p.Asn93Ser | missense_variant | 5/9 | ENST00000434687.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IKZF2 | ENST00000434687.6 | c.278A>G | p.Asn93Ser | missense_variant | 5/9 | 5 | NM_001387220.1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00730 AC: 1109AN: 152012Hom.: 11 Cov.: 32
GnomAD3 exomes AF: 0.00637 AC: 1599AN: 250986Hom.: 13 AF XY: 0.00686 AC XY: 931AN XY: 135624
GnomAD4 exome AF: 0.00608 AC: 8887AN: 1461708Hom.: 52 Cov.: 31 AF XY: 0.00636 AC XY: 4625AN XY: 727144
GnomAD4 genome ? AF: 0.00732 AC: 1113AN: 152130Hom.: 11 Cov.: 32 AF XY: 0.00686 AC XY: 510AN XY: 74374
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | IKZF2: BP4, BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 01, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at