chr22-23573302-G-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_020070.4(IGLL1):c.606C>G(p.Thr202=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000171 in 1,461,704 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. T202T) has been classified as Likely benign.
Frequency
Consequence
NM_020070.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IGLL1 | NM_020070.4 | c.606C>G | p.Thr202= | synonymous_variant | 3/3 | ENST00000330377.3 | |
IGLL1 | NM_001369906.1 | c.609C>G | p.Thr203= | synonymous_variant | 3/3 | ||
IGLL1 | NM_152855.3 | c.*235C>G | 3_prime_UTR_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGLL1 | ENST00000330377.3 | c.606C>G | p.Thr202= | synonymous_variant | 3/3 | 1 | NM_020070.4 | P1 | |
IGLL1 | ENST00000249053.3 | c.*235C>G | 3_prime_UTR_variant | 2/2 | 1 | ||||
ENST00000458318.2 | n.391-163G>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461704Hom.: 0 Cov.: 32 AF XY: 0.0000193 AC XY: 14AN XY: 727160
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Agammaglobulinemia 2, autosomal recessive Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 20, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at