19-49951938-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_052884.3(SIGLEC11):c.1783G>A(p.Ala595Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000439 in 1,458,818 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 (★).
Frequency
Consequence
NM_052884.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SIGLEC11 | ENST00000447370.6 | c.1783G>A | p.Ala595Thr | missense_variant | Exon 10 of 11 | 1 | NM_052884.3 | ENSP00000412361.2 | ||
ENSG00000269179 | ENST00000451973.1 | n.*30G>A | non_coding_transcript_exon_variant | Exon 2 of 3 | 2 | ENSP00000391489.1 | ||||
ENSG00000269179 | ENST00000451973.1 | n.*30G>A | 3_prime_UTR_variant | Exon 2 of 3 | 2 | ENSP00000391489.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000405 AC: 1AN: 247116Hom.: 0 AF XY: 0.00000748 AC XY: 1AN XY: 133690
GnomAD4 exome AF: 0.0000439 AC: 64AN: 1458818Hom.: 0 Cov.: 31 AF XY: 0.0000469 AC XY: 34AN XY: 725698
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1783G>A (p.A595T) alteration is located in exon 10 (coding exon 10) of the SIGLEC11 gene. This alteration results from a G to A substitution at nucleotide position 1783, causing the alanine (A) at amino acid position 595 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