rs187264712
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6BS2_Supporting
The NM_000313.4(PROS1):c.234+5G>A variant causes a splice region, intron change. The variant allele was found at a frequency of 0.0008 in 1,612,214 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000313.4 splice_region, intron
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 |
---|---|---|---|---|---|---|---|---|
PROS1 | NM_000313.4 | c.234+5G>A | splice_region_variant, intron_variant | Intron 2 of 14 | ENST00000394236.9 | NP_000304.2 | ||
PROS1 | NM_001314077.2 | c.330+5G>A | splice_region_variant, intron_variant | Intron 3 of 15 | NP_001301006.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00116 AC: 176AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00152 AC: 382AN: 251300Hom.: 0 AF XY: 0.00149 AC XY: 203AN XY: 135856
GnomAD4 exome AF: 0.000762 AC: 1113AN: 1459912Hom.: 2 Cov.: 31 AF XY: 0.000753 AC XY: 547AN XY: 726250
GnomAD4 genome AF: 0.00116 AC: 176AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.00146 AC XY: 109AN XY: 74460
ClinVar
Submissions by phenotype
not provided Uncertain:1
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Thrombophilia due to protein S deficiency, autosomal recessive Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at