chr2-240630209-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005301.5(GPR35):c.257C>T(p.Thr86Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000127 in 1,574,148 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. T86T) has been classified as Likely benign.
Frequency
Consequence
NM_005301.5 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 | UniProt |
---|---|---|---|---|---|---|---|
GPR35 | NM_005301.5 | c.257C>T | p.Thr86Met | missense_variant | 2/2 | ENST00000407714.2 | |
GPR35 | NM_001195381.3 | c.350C>T | p.Thr117Met | missense_variant | 6/6 | ||
GPR35 | NM_001195382.3 | c.350C>T | p.Thr117Met | missense_variant | 6/6 | ||
GPR35 | NM_001394730.1 | c.350C>T | p.Thr117Met | missense_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR35 | ENST00000407714.2 | c.257C>T | p.Thr86Met | missense_variant | 2/2 | 1 | NM_005301.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152244Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000176 AC: 4AN: 226810Hom.: 0 AF XY: 0.0000326 AC XY: 4AN XY: 122758
GnomAD4 exome AF: 0.0000113 AC: 16AN: 1421904Hom.: 0 Cov.: 34 AF XY: 0.0000114 AC XY: 8AN XY: 703022
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152244Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 13, 2023 | The c.350C>T (p.T117M) alteration is located in exon 6 (coding exon 2) of the GPR35 gene. This alteration results from a C to T substitution at nucleotide position 350, causing the threonine (T) at amino acid position 117 to be replaced by a methionine (M). 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