chr20-3689187-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_023068.4(SIGLEC1):c.5038G>A(p.Val1680Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,860 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_023068.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SIGLEC1 | NM_023068.4 | c.5038G>A | p.Val1680Met | missense_variant | 21/22 | ENST00000344754.6 | |
SIGLEC1 | NM_001367089.1 | c.4997+413G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SIGLEC1 | ENST00000344754.6 | c.5038G>A | p.Val1680Met | missense_variant | 21/22 | 1 | NM_023068.4 | P2 | |
SIGLEC1 | ENST00000419548.4 | c.*719G>A | 3_prime_UTR_variant | 5/5 | 2 | ||||
SIGLEC1 | ENST00000707083.1 | c.4997+413G>A | intron_variant | A2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251480Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135912
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461860Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727236
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 13, 2023 | The c.5038G>A (p.V1680M) alteration is located in exon 20 (coding exon 20) of the SIGLEC1 gene. This alteration results from a G to A substitution at nucleotide position 5038, causing the valine (V) at amino acid position 1680 to be replaced by a methionine (M). 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