rs376437604
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000467482.6(GPR143):c.456-9G>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000276 in 1,142,589 control chromosomes in the GnomAD database, including 1 homozygotes. There are 91 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
ENST00000467482.6 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPR143 | NM_000273.3 | c.456-9G>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000467482.6 | NP_000264.2 | |||
GPR143 | XM_005274541.4 | c.456-9G>C | splice_polypyrimidine_tract_variant, intron_variant | XP_005274598.1 | ||||
GPR143 | XM_024452388.2 | c.204-9G>C | splice_polypyrimidine_tract_variant, intron_variant | XP_024308156.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPR143 | ENST00000467482.6 | c.456-9G>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000273.3 | ENSP00000417161 | P1 | |||
GPR143 | ENST00000431126.1 | c.204-9G>C | splice_polypyrimidine_tract_variant, intron_variant | 3 | ENSP00000406138 | |||||
GPR143 | ENST00000447366.5 | c.204-9G>C | splice_polypyrimidine_tract_variant, intron_variant | 3 | ENSP00000390546 | |||||
GPR143 | ENST00000480178.1 | n.64-9G>C | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00134 AC: 150AN: 112258Hom.: 1 Cov.: 23 AF XY: 0.00122 AC XY: 42AN XY: 34422
GnomAD3 exomes AF: 0.000366 AC: 64AN: 175102Hom.: 0 AF XY: 0.000196 AC XY: 12AN XY: 61264
GnomAD4 exome AF: 0.000161 AC: 166AN: 1030278Hom.: 0 Cov.: 25 AF XY: 0.000161 AC XY: 49AN XY: 304222
GnomAD4 genome AF: 0.00133 AC: 149AN: 112311Hom.: 1 Cov.: 23 AF XY: 0.00122 AC XY: 42AN XY: 34485
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 11, 2023 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at