rs760572663
Variant summary
Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4
The NM_001243439.2(SPECC1):c.881C>G(p.Ser294Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000109 in 1,461,802 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001243439.2 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Uncertain_significance. The variant received 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPECC1 | NM_001243439.2 | c.881C>G | p.Ser294Cys | missense_variant | Exon 4 of 15 | ENST00000395527.9 | NP_001230368.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD2 exomes AF: 0.0000160 AC: 4AN: 250634 AF XY: 0.0000148 show subpopulations
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461802Hom.: 0 Cov.: 63 AF XY: 0.0000151 AC XY: 11AN XY: 727200 show subpopulations
Age Distribution
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.881C>G (p.S294C) alteration is located in exon 1 (coding exon 1) of the SPECC1 gene. This alteration results from a C to G substitution at nucleotide position 881, causing the serine (S) at amino acid position 294 to be replaced by a cysteine (C). 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