chr8-117146954-T-C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_173851.3(SLC30A8):c.72T>C(p.Ser24=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000568 in 1,613,828 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_173851.3 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC30A8 | NM_173851.3 | c.72T>C | p.Ser24= | splice_region_variant, synonymous_variant | 2/8 | ENST00000456015.7 | |
LOC105375716 | XR_007061067.1 | n.819+25661A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC30A8 | ENST00000456015.7 | c.72T>C | p.Ser24= | splice_region_variant, synonymous_variant | 2/8 | 1 | NM_173851.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00302 AC: 459AN: 152104Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.000808 AC: 203AN: 251084Hom.: 2 AF XY: 0.000553 AC XY: 75AN XY: 135740
GnomAD4 exome AF: 0.000313 AC: 457AN: 1461608Hom.: 4 Cov.: 31 AF XY: 0.000281 AC XY: 204AN XY: 727102
GnomAD4 genome ? AF: 0.00302 AC: 460AN: 152220Hom.: 6 Cov.: 32 AF XY: 0.00300 AC XY: 223AN XY: 74432
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 08, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at