chr5-102258045-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_180991.5(SLCO4C1):āc.1171A>Gā(p.Thr391Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000656 in 1,600,702 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 (ā ).
Frequency
Consequence
NM_180991.5 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 |
---|---|---|---|---|---|---|---|
SLCO4C1 | NM_180991.5 | c.1171A>G | p.Thr391Ala | missense_variant | 7/13 | ENST00000310954.7 | |
SLCO4C1 | XM_011543370.3 | c.907A>G | p.Thr303Ala | missense_variant | 6/12 | ||
SLCO4C1 | XM_011543372.2 | c.757A>G | p.Thr253Ala | missense_variant | 9/15 | ||
SLCO4C1 | XM_047417146.1 | c.757A>G | p.Thr253Ala | missense_variant | 9/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLCO4C1 | ENST00000310954.7 | c.1171A>G | p.Thr391Ala | missense_variant | 7/13 | 1 | NM_180991.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000126 AC: 3AN: 237832Hom.: 0 AF XY: 0.0000156 AC XY: 2AN XY: 128456
GnomAD4 exome AF: 0.0000642 AC: 93AN: 1448576Hom.: 0 Cov.: 29 AF XY: 0.0000583 AC XY: 42AN XY: 720006
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 20, 2023 | The c.1171A>G (p.T391A) alteration is located in exon 7 (coding exon 7) of the SLCO4C1 gene. This alteration results from a A to G substitution at nucleotide position 1171, causing the threonine (T) at amino acid position 391 to be replaced by an alanine (A). 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