rs111903752
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_020070.4(IGLL1):āc.485T>Cā(p.Met162Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000755 in 1,613,832 control chromosomes in the GnomAD database, including 26 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 (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M162K) has been classified as Benign.
Frequency
Consequence
NM_020070.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IGLL1 | NM_020070.4 | c.485T>C | p.Met162Thr | missense_variant | 3/3 | ENST00000330377.3 | |
IGLL1 | NM_001369906.1 | c.488T>C | p.Met163Thr | missense_variant | 3/3 | ||
IGLL1 | NM_152855.3 | c.*114T>C | 3_prime_UTR_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGLL1 | ENST00000330377.3 | c.485T>C | p.Met162Thr | missense_variant | 3/3 | 1 | NM_020070.4 | P1 | |
IGLL1 | ENST00000249053.3 | c.*114T>C | 3_prime_UTR_variant | 2/2 | 1 | ||||
ENST00000458318.2 | n.391-42A>G | intron_variant, non_coding_transcript_variant | 3 | ||||||
IGLL1 | ENST00000438703.1 | c.488T>C | p.Met163Thr | missense_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000559 AC: 85AN: 152090Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00156 AC: 392AN: 251276Hom.: 8 AF XY: 0.00205 AC XY: 278AN XY: 135798
GnomAD4 exome AF: 0.000776 AC: 1134AN: 1461626Hom.: 25 Cov.: 33 AF XY: 0.00112 AC XY: 811AN XY: 727136
GnomAD4 genome ? AF: 0.000558 AC: 85AN: 152206Hom.: 1 Cov.: 32 AF XY: 0.000739 AC XY: 55AN XY: 74406
ClinVar
Submissions by phenotype
Agammaglobulinemia 2, autosomal recessive Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 21, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at