chr2-240630353-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.401C>T(p.Ala134Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000474 in 1,603,958 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
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.401C>T | p.Ala134Val | missense_variant | 2/2 | ENST00000407714.2 | |
GPR35 | NM_001195381.3 | c.494C>T | p.Ala165Val | missense_variant | 6/6 | ||
GPR35 | NM_001195382.3 | c.494C>T | p.Ala165Val | missense_variant | 6/6 | ||
GPR35 | NM_001394730.1 | c.494C>T | p.Ala165Val | missense_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR35 | ENST00000407714.2 | c.401C>T | p.Ala134Val | missense_variant | 2/2 | 1 | NM_005301.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000985 AC: 15AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000550 AC: 13AN: 236534Hom.: 0 AF XY: 0.0000615 AC XY: 8AN XY: 130116
GnomAD4 exome AF: 0.0000420 AC: 61AN: 1451624Hom.: 0 Cov.: 39 AF XY: 0.0000471 AC XY: 34AN XY: 721972
GnomAD4 genome ? AF: 0.0000985 AC: 15AN: 152334Hom.: 0 Cov.: 33 AF XY: 0.0000805 AC XY: 6AN XY: 74490
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 12, 2022 | The c.494C>T (p.A165V) 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 494, causing the alanine (A) at amino acid position 165 to be replaced by a valine (V). 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