chr19-51531439-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001245.7(SIGLEC6):c.148C>T(p.Pro50Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000137 in 1,613,986 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_001245.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SIGLEC6 | NM_001245.7 | c.148C>T | p.Pro50Ser | missense_variant | 2/8 | ENST00000425629.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SIGLEC6 | ENST00000425629.8 | c.148C>T | p.Pro50Ser | missense_variant | 2/8 | 2 | NM_001245.7 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000639 AC: 16AN: 250486Hom.: 0 AF XY: 0.0000811 AC XY: 11AN XY: 135686
GnomAD4 exome AF: 0.000140 AC: 204AN: 1461858Hom.: 0 Cov.: 36 AF XY: 0.000113 AC XY: 82AN XY: 727232
GnomAD4 genome ? AF: 0.000112 AC: 17AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 20, 2023 | The c.148C>T (p.P50S) alteration is located in exon 2 (coding exon 2) of the SIGLEC6 gene. This alteration results from a C to T substitution at nucleotide position 148, causing the proline (P) at amino acid position 50 to be replaced by a serine (S). 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