chr3-36380662-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003149.3(STAC):c.19C>T(p.Pro7Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000325 in 1,599,292 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003149.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000361 AC: 8AN: 221408Hom.: 0 AF XY: 0.0000416 AC XY: 5AN XY: 120282
GnomAD4 exome AF: 0.0000187 AC: 27AN: 1447128Hom.: 0 Cov.: 32 AF XY: 0.0000209 AC XY: 15AN XY: 718260
GnomAD4 genome AF: 0.000164 AC: 25AN: 152164Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.19C>T (p.P7S) alteration is located in exon 1 (coding exon 1) of the STAC gene. This alteration results from a C to T substitution at nucleotide position 19, causing the proline (P) at amino acid position 7 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