18-45838852-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_213602.3(SIGLEC15):c.631G>A(p.Val211Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000202 in 1,575,652 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_213602.3 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 |
---|---|---|---|---|---|---|---|
SIGLEC15 | NM_213602.3 | c.631G>A | p.Val211Met | missense_variant | 4/6 | ENST00000389474.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SIGLEC15 | ENST00000389474.8 | c.631G>A | p.Val211Met | missense_variant | 4/6 | 1 | NM_213602.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000374 AC: 57AN: 152214Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000250 AC: 45AN: 179888Hom.: 0 AF XY: 0.000210 AC XY: 21AN XY: 99788
GnomAD4 exome AF: 0.000183 AC: 261AN: 1423438Hom.: 0 Cov.: 30 AF XY: 0.000177 AC XY: 125AN XY: 706124
GnomAD4 genome ? AF: 0.000374 AC: 57AN: 152214Hom.: 0 Cov.: 33 AF XY: 0.000350 AC XY: 26AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 20, 2021 | The c.631G>A (p.V211M) alteration is located in exon 4 (coding exon 4) of the SIGLEC15 gene. This alteration results from a G to A substitution at nucleotide position 631, causing the valine (V) at amino acid position 211 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