chr3-133934714-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM4
The NM_005630.3(SLCO2A1):āc.1931G>Cā(p.Ter644Serext*?) variant causes a stop lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,611,686 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 (ā ).
Frequency
Consequence
NM_005630.3 stop_lost
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLCO2A1 | ENST00000310926.11 | c.1931G>C | p.Ter644Serext*? | stop_lost | Exon 14 of 14 | 1 | NM_005630.3 | ENSP00000311291.4 | ||
SLCO2A1 | ENST00000493729.5 | c.1703G>C | p.Ter568Serext*? | stop_lost | Exon 13 of 13 | 5 | ENSP00000418893.1 | |||
SLCO2A1 | ENST00000481359.3 | n.*493G>C | non_coding_transcript_exon_variant | Exon 13 of 13 | 5 | ENSP00000420028.3 | ||||
SLCO2A1 | ENST00000481359.3 | n.*493G>C | 3_prime_UTR_variant | Exon 13 of 13 | 5 | ENSP00000420028.3 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 250370Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135392
GnomAD4 exome AF: 0.00000480 AC: 7AN: 1459476Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726220
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74362
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change disrupts the translational stop signal of the SLCO2A1 mRNA. It is expected to extend the length of the SLCO2A1 protein by 59 additional amino acid residues. This variant is present in population databases (rs149529847, gnomAD 0.02%). This protein extension has been observed in individual(s) with clinical features of hypertrophic osteoarthropathy (internal data). ClinVar contains an entry for this variant (Variation ID: 1438342). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at