chrX-9765656-G-A
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_000273.3(GPR143):c.162C>T(p.Pro54Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000297 in 874,297 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 9 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 25)
Exomes 𝑓: 0.000030 ( 0 hom. 9 hem. )
Consequence
GPR143
NM_000273.3 synonymous
NM_000273.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.379
Genes affected
GPR143 (HGNC:20145): (G protein-coupled receptor 143) This gene encodes a protein that binds to heterotrimeric G proteins and is targeted to melanosomes in pigment cells. This protein is thought to be involved in intracellular signal transduction mechanisms. Mutations in this gene cause ocular albinism type 1, also referred to as Nettleship-Falls type ocular albinism, a severe visual disorder. A related pseudogene has been identified on chromosome Y. [provided by RefSeq, Dec 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
Variant X-9765656-G-A is Benign according to our data. Variant chrX-9765656-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 435350.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.379 with no splicing effect.
BS2
High Hemizygotes in GnomAdExome4 at 9 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPR143 | NM_000273.3 | c.162C>T | p.Pro54Pro | synonymous_variant | 1/9 | ENST00000467482.6 | NP_000264.2 | |
GPR143 | XM_005274541.4 | c.162C>T | p.Pro54Pro | synonymous_variant | 1/9 | XP_005274598.1 | ||
GPR143 | XM_024452388.2 | c.-2-4830C>T | intron_variant | XP_024308156.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPR143 | ENST00000467482.6 | c.162C>T | p.Pro54Pro | synonymous_variant | 1/9 | 1 | NM_000273.3 | ENSP00000417161.1 | ||
GPR143 | ENST00000447366.5 | c.-2-4830C>T | intron_variant | 3 | ENSP00000390546.2 | |||||
GPR143 | ENST00000431126.1 | c.-3+464C>T | intron_variant | 3 | ENSP00000406138.1 |
Frequencies
GnomAD3 genomes Cov.: 25
GnomAD3 genomes
Cov.:
25
GnomAD4 exome AF: 0.0000297 AC: 26AN: 874297Hom.: 0 Cov.: 27 AF XY: 0.0000331 AC XY: 9AN XY: 271625
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874297
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GnomAD4 genome Cov.: 25
GnomAD4 genome
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25
Bravo
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 09, 2016 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at