chrX-9725844-G-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_000273.3(GPR143):c.1121-4C>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000249 in 1,204,935 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000273.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPR143 | NM_000273.3 | c.1121-4C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000467482.6 | |||
GPR143 | XM_005274541.4 | c.*92C>G | 3_prime_UTR_variant | 9/9 | |||
GPR143 | XM_024452388.2 | c.869-4C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR143 | ENST00000467482.6 | c.1121-4C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000273.3 | P1 | |||
TBL1X | ENST00000647060.1 | c.1554+10841G>C | intron_variant |
Frequencies
GnomAD3 genomes AF: 0.00000907 AC: 1AN: 110263Hom.: 0 Cov.: 21 AF XY: 0.0000308 AC XY: 1AN XY: 32469
GnomAD3 exomes AF: 0.00000566 AC: 1AN: 176786Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 61646
GnomAD4 exome AF: 0.00000183 AC: 2AN: 1094672Hom.: 0 Cov.: 29 AF XY: 0.00000278 AC XY: 1AN XY: 360156
GnomAD4 genome AF: 0.00000907 AC: 1AN: 110263Hom.: 0 Cov.: 21 AF XY: 0.0000308 AC XY: 1AN XY: 32469
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 15, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at