chr12-7135836-A-C
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014718.4(CLSTN3):c.625A>C(p.Ser209Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000031 in 1,613,140 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_014718.4 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLSTN3 | NM_014718.4 | c.625A>C | p.Ser209Arg | missense_variant | Exon 5 of 18 | ENST00000266546.11 | NP_055533.2 | |
CLSTN3 | XM_047429919.1 | c.868A>C | p.Ser290Arg | missense_variant | Exon 6 of 19 | XP_047285875.1 | ||
CLSTN3 | XM_047429920.1 | c.625A>C | p.Ser209Arg | missense_variant | Exon 6 of 19 | XP_047285876.1 | ||
CLSTN3 | XM_047429921.1 | c.625A>C | p.Ser209Arg | missense_variant | Exon 6 of 19 | XP_047285877.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CLSTN3 | ENST00000266546.11 | c.625A>C | p.Ser209Arg | missense_variant | Exon 5 of 18 | 1 | NM_014718.4 | ENSP00000266546.6 | ||
CLSTN3 | ENST00000537408.1 | n.1199A>C | non_coding_transcript_exon_variant | Exon 4 of 17 | 1 | |||||
CLSTN3 | ENST00000540931.1 | n.120A>C | non_coding_transcript_exon_variant | Exon 2 of 4 | 2 | |||||
CLSTN3 | ENST00000541667.5 | n.352A>C | non_coding_transcript_exon_variant | Exon 4 of 6 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152170Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.00000399 AC: 1AN: 250364 AF XY: 0.00 show subpopulations
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1460970Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 726782 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74340 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
Age Distribution
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at