17-20096785-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001243439.2(SPECC1):c.134C>T(p.Ser45Phe) variant causes a missense change. The variant allele was found at a frequency of 0.0000998 in 1,613,522 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPECC1 | NM_001243439.2 | c.134C>T | p.Ser45Phe | missense_variant | Exon 2 of 15 | ENST00000395527.9 | NP_001230368.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152138Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000195 AC: 49AN: 250864Hom.: 0 AF XY: 0.000199 AC XY: 27AN XY: 135572
GnomAD4 exome AF: 0.0000972 AC: 142AN: 1461384Hom.: 0 Cov.: 29 AF XY: 0.000100 AC XY: 73AN XY: 726914
GnomAD4 genome AF: 0.000125 AC: 19AN: 152138Hom.: 0 Cov.: 33 AF XY: 0.000175 AC XY: 13AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.134C>T (p.S45F) alteration is located in exon 1 (coding exon 1) of the SPECC1 gene. This alteration results from a C to T substitution at nucleotide position 134, causing the serine (S) at amino acid position 45 to be replaced by a phenylalanine (F). 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