5-102247339-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_180991.5(SLCO4C1):c.1724C>T(p.Ala575Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000625 in 1,598,754 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_180991.5 missense
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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLCO4C1 | NM_180991.5 | c.1724C>T | p.Ala575Val | missense_variant | 10/13 | ENST00000310954.7 | NP_851322.3 | |
SLCO4C1 | XM_011543370.3 | c.1460C>T | p.Ala487Val | missense_variant | 9/12 | XP_011541672.1 | ||
SLCO4C1 | XM_011543372.2 | c.1310C>T | p.Ala437Val | missense_variant | 12/15 | XP_011541674.1 | ||
SLCO4C1 | XM_047417146.1 | c.1310C>T | p.Ala437Val | missense_variant | 12/15 | XP_047273102.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLCO4C1 | ENST00000310954.7 | c.1724C>T | p.Ala575Val | missense_variant | 10/13 | 1 | NM_180991.5 | ENSP00000309741 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152054Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000320 AC: 8AN: 249996Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135104
GnomAD4 exome AF: 0.0000650 AC: 94AN: 1446700Hom.: 0 Cov.: 30 AF XY: 0.0000543 AC XY: 39AN XY: 717894
GnomAD4 genome AF: 0.0000395 AC: 6AN: 152054Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74278
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 17, 2022 | The c.1724C>T (p.A575V) alteration is located in exon 10 (coding exon 10) of the SLCO4C1 gene. This alteration results from a C to T substitution at nucleotide position 1724, causing the alanine (A) at amino acid position 575 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