chr20-3688615-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_023068.4(SIGLEC1):āc.5075T>Cā(p.Ile1692Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000692 in 1,445,250 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 Uncertain significance (ā ).
Frequency
Consequence
NM_023068.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SIGLEC1 | NM_023068.4 | c.5075T>C | p.Ile1692Thr | missense_variant | 22/22 | ENST00000344754.6 | |
SIGLEC1 | NM_001367089.1 | c.5002T>C | p.Leu1668= | synonymous_variant | 20/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SIGLEC1 | ENST00000344754.6 | c.5075T>C | p.Ile1692Thr | missense_variant | 22/22 | 1 | NM_023068.4 | P2 | |
SIGLEC1 | ENST00000707083.1 | c.5002T>C | p.Leu1668= | synonymous_variant | 20/20 | A2 | |||
SIGLEC1 | ENST00000419548.4 | c.*1291T>C | 3_prime_UTR_variant | 5/5 | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.92e-7 AC: 1AN: 1445250Hom.: 0 Cov.: 30 AF XY: 0.00000139 AC XY: 1AN XY: 717174
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 22, 2023 | The c.5075T>C (p.I1692T) alteration is located in exon 21 (coding exon 21) of the SIGLEC1 gene. This alteration results from a T to C substitution at nucleotide position 5075, causing the isoleucine (I) at amino acid position 1692 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at