chr15-92162897-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_013272.4(SLCO3A1):c.1895C>T(p.Ala632Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000142 in 1,614,084 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_013272.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLCO3A1 | NM_013272.4 | c.1895C>T | p.Ala632Val | missense_variant | 10/10 | ENST00000318445.11 | |
SLCO3A1 | NM_001145044.1 | c.1895C>T | p.Ala632Val | missense_variant | 10/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLCO3A1 | ENST00000318445.11 | c.1895C>T | p.Ala632Val | missense_variant | 10/10 | 1 | NM_013272.4 | P1 | |
ENST00000557683.1 | n.440G>A | non_coding_transcript_exon_variant | 2/2 | 4 | |||||
ENST00000561674.1 | n.186-5656G>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152190Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251466Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135902
GnomAD4 exome AF: 0.0000150 AC: 22AN: 1461894Hom.: 0 Cov.: 30 AF XY: 0.00000963 AC XY: 7AN XY: 727248
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152190Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 03, 2022 | The c.1895C>T (p.A632V) alteration is located in exon 10 (coding exon 10) of the SLCO3A1 gene. This alteration results from a C to T substitution at nucleotide position 1895, causing the alanine (A) at amino acid position 632 to be replaced by a valine (V). 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