chr6-3283860-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_015482.2(SLC22A23):c.1695G>A(p.Thr565=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00104 in 1,613,758 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. T565T) has been classified as Likely benign.
Frequency
Consequence
NM_015482.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC22A23 | NM_015482.2 | c.1695G>A | p.Thr565= | synonymous_variant | 9/10 | ENST00000406686.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC22A23 | ENST00000406686.8 | c.1695G>A | p.Thr565= | synonymous_variant | 9/10 | 5 | NM_015482.2 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00464 AC: 707AN: 152214Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00134 AC: 336AN: 250930Hom.: 0 AF XY: 0.00104 AC XY: 141AN XY: 135760
GnomAD4 exome AF: 0.000660 AC: 965AN: 1461426Hom.: 11 Cov.: 31 AF XY: 0.000585 AC XY: 425AN XY: 727008
GnomAD4 genome AF: 0.00465 AC: 708AN: 152332Hom.: 5 Cov.: 32 AF XY: 0.00493 AC XY: 367AN XY: 74488
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 09, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at