chr20-3691442-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_023068.4(SIGLEC1):c.4489G>A(p.Ala1497Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,613,288 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_023068.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SIGLEC1 | NM_023068.4 | c.4489G>A | p.Ala1497Thr | missense_variant | 18/22 | ENST00000344754.6 | |
SIGLEC1 | NM_001367089.1 | c.4489G>A | p.Ala1497Thr | missense_variant | 17/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SIGLEC1 | ENST00000344754.6 | c.4489G>A | p.Ala1497Thr | missense_variant | 18/22 | 1 | NM_023068.4 | P2 | |
SIGLEC1 | ENST00000707083.1 | c.4489G>A | p.Ala1497Thr | missense_variant | 17/20 | A2 | |||
SIGLEC1 | ENST00000419548.4 | c.931G>A | p.Ala311Thr | missense_variant | 4/5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152238Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250568Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135712
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1460932Hom.: 0 Cov.: 33 AF XY: 0.0000110 AC XY: 8AN XY: 726780
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152356Hom.: 0 Cov.: 33 AF XY: 0.0000268 AC XY: 2AN XY: 74502
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 08, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at