rs118144424
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_021615.5(CHST6):c.294C>T(p.Ser98=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000411 in 1,460,706 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. S98S) has been classified as Benign.
Frequency
Consequence
NM_021615.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHST6 | NM_021615.5 | c.294C>T | p.Ser98= | synonymous_variant | 3/3 | ENST00000332272.9 | |
CHST6 | NR_163480.1 | n.733+2282C>T | intron_variant, non_coding_transcript_variant | ||||
CHST6 | NR_163481.1 | n.577+2282C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHST6 | ENST00000332272.9 | c.294C>T | p.Ser98= | synonymous_variant | 3/3 | 3 | NM_021615.5 | P1 | |
ENST00000530512.3 | n.425+3215G>A | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000802 AC: 2AN: 249482Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135476
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1460706Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 726684
GnomAD4 genome ? Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at