19-51520213-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001245.7(SIGLEC6):c.1231C>A(p.Pro411Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000199 in 1,605,938 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/17 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SIGLEC6 | NM_001245.7 | c.1231C>A | p.Pro411Thr | missense_variant | 8/8 | ENST00000425629.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SIGLEC6 | ENST00000425629.8 | c.1231C>A | p.Pro411Thr | missense_variant | 8/8 | 2 | NM_001245.7 | P2 | |
ENST00000598220.1 | n.383G>T | non_coding_transcript_exon_variant | 2/2 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000722 AC: 18AN: 249268Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135226
GnomAD4 exome AF: 0.0000179 AC: 26AN: 1453804Hom.: 0 Cov.: 30 AF XY: 0.0000166 AC XY: 12AN XY: 722512
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2023 | The c.1231C>A (p.P411T) alteration is located in exon 8 (coding exon 8) of the SIGLEC6 gene. This alteration results from a C to A substitution at nucleotide position 1231, causing the proline (P) at amino acid position 411 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