chr6-43304703-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_153320.2(SLC22A7):c.1625C>T(p.Pro542Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000194 in 1,595,130 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_153320.2 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC22A7 | NM_153320.2 | c.1625C>T | p.Pro542Leu | missense_variant | 11/11 | ENST00000372585.10 | NP_696961.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC22A7 | ENST00000372585.10 | c.1625C>T | p.Pro542Leu | missense_variant | 11/11 | 5 | NM_153320.2 | ENSP00000361666 | A1 | |
SLC22A7 | ENST00000372589.7 | c.1619C>T | p.Pro540Leu | missense_variant | 10/10 | 2 | ENSP00000361670 | P4 | ||
CRIP3 | ENST00000416431.5 | c.323+1364G>A | intron_variant | 3 | ENSP00000414553 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152134Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000415 AC: 1AN: 240776Hom.: 0 AF XY: 0.00000767 AC XY: 1AN XY: 130452
GnomAD4 exome AF: 0.0000208 AC: 30AN: 1442996Hom.: 0 Cov.: 30 AF XY: 0.0000251 AC XY: 18AN XY: 715816
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152134Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2024 | The c.1625C>T (p.P542L) alteration is located in exon 11 (coding exon 11) of the SLC22A7 gene. This alteration results from a C to T substitution at nucleotide position 1625, causing the proline (P) at amino acid position 542 to be replaced by a leucine (L). 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