NM_053003.4:c.1510T>C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_053003.4(SIGLEC12):c.1510T>C(p.Ser504Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,613,078 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_053003.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SIGLEC12 | ENST00000291707.8 | c.1510T>C | p.Ser504Pro | missense_variant | Exon 7 of 8 | 1 | NM_053003.4 | ENSP00000291707.3 | ||
SIGLEC12 | ENST00000596742.1 | n.*725T>C | non_coding_transcript_exon_variant | Exon 7 of 8 | 1 | ENSP00000469791.1 | ||||
SIGLEC12 | ENST00000596742.1 | n.*725T>C | 3_prime_UTR_variant | Exon 7 of 8 | 1 | ENSP00000469791.1 | ||||
SIGLEC12 | ENST00000598614.1 | c.1156T>C | p.Ser386Pro | missense_variant | Exon 6 of 7 | 5 | ENSP00000472873.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152052Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251468Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135904
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460908Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726782
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74392
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1510T>C (p.S504P) alteration is located in exon 7 (coding exon 7) of the SIGLEC12 gene. This alteration results from a T to C substitution at nucleotide position 1510, causing the serine (S) at amino acid position 504 to be replaced by a proline (P). 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