chr22-23573423-A-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_020070.4(IGLL1):c.485T>A(p.Met162Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0272 in 1,613,580 control chromosomes in the GnomAD database, including 771 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 variant affecting the same amino acid position, but resulting in a different missense (i.e. M162T) has been classified as Benign.
Frequency
Consequence
NM_020070.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IGLL1 | NM_020070.4 | c.485T>A | p.Met162Lys | missense_variant | 3/3 | ENST00000330377.3 | |
IGLL1 | NM_001369906.1 | c.488T>A | p.Met163Lys | missense_variant | 3/3 | ||
IGLL1 | NM_152855.3 | c.*114T>A | 3_prime_UTR_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGLL1 | ENST00000330377.3 | c.485T>A | p.Met162Lys | missense_variant | 3/3 | 1 | NM_020070.4 | P1 | |
IGLL1 | ENST00000249053.3 | c.*114T>A | 3_prime_UTR_variant | 2/2 | 1 | ||||
ENST00000458318.2 | n.391-42A>T | intron_variant, non_coding_transcript_variant | 3 | ||||||
IGLL1 | ENST00000438703.1 | c.488T>A | p.Met163Lys | missense_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0393 AC: 5980AN: 152058Hom.: 152 Cov.: 32
GnomAD3 exomes AF: 0.0305 AC: 7661AN: 251276Hom.: 150 AF XY: 0.0302 AC XY: 4100AN XY: 135798
GnomAD4 exome AF: 0.0260 AC: 37979AN: 1461406Hom.: 619 Cov.: 33 AF XY: 0.0260 AC XY: 18898AN XY: 727018
GnomAD4 genome AF: 0.0393 AC: 5985AN: 152174Hom.: 152 Cov.: 32 AF XY: 0.0393 AC XY: 2920AN XY: 74388
ClinVar
Submissions by phenotype
Agammaglobulinemia 2, autosomal recessive Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 22, 2023 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 09, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at