Variant X-9743555-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000273.3(GPR143):c.767+10C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 1,012,845 control chromosomes in the GnomAD database, including 17,349 homozygotes. There are 67,243 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.17 ( 1385 hom., 5467 hem., cov: 22)

Exomes 𝑓: 0.22 ( 15964 hom. 61776 hem. )

Consequence

GPR143
NM_000273.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -0.347

Variant links:

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]

GPR143 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant X-9743555-G-C is Benign according to our data. Variant chrX-9743555-G-C is described in ClinVar as [Benign]. Clinvar id is 255712.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-9743555-G-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
GPR143	NM_000273.3 linkuse as main transcript	c.767+10C>G	intron_variant	ENST00000467482.6	NP_000264.2
GPR143	XM_005274541.4 linkuse as main transcript	c.767+10C>G	intron_variant		XP_005274598.1
GPR143	XM_024452388.2 linkuse as main transcript	c.515+10C>G	intron_variant		XP_024308156.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
GPR143	ENST00000467482.6 linkuse as main transcript	c.767+10C>G	intron_variant	1	NM_000273.3	ENSP00000417161	P1
GPR143	ENST00000447366.5 linkuse as main transcript	c.515+10C>G	intron_variant	3		ENSP00000390546
GPR143	ENST00000431126.1 linkuse as main transcript		downstream_gene_variant	3		ENSP00000406138

Frequencies

GnomAD3 genomes

AF:

0.170

AC:

18893

AN:

110810

Hom.:

1384

Cov.:

AF XY:

0.165

AC XY:

5460

AN XY:

33072

show subpopulations

Gnomad AFR

AF:

0.0619

Gnomad AMI

AF:

0.243

Gnomad AMR

AF:

0.112

Gnomad ASJ

AF:

0.275

Gnomad EAS

AF:

0.228

Gnomad SAS

AF:

0.320

Gnomad FIN

AF:

0.205

Gnomad MID

AF:

0.242

Gnomad NFE

AF:

0.223

Gnomad OTH

AF:

0.177

GnomAD3 exomes

AF:

0.203

AC:

37159

AN:

182915

Hom.:

2562

AF XY:

0.221

AC XY:

14883

AN XY:

67399

show subpopulations

Gnomad AFR exome

AF:

0.0616

Gnomad AMR exome

AF:

0.0731

Gnomad ASJ exome

AF:

0.285

Gnomad EAS exome

AF:

0.238

Gnomad SAS exome

AF:

0.332

Gnomad FIN exome

AF:

0.210

Gnomad NFE exome

AF:

0.224

Gnomad OTH exome

AF:

0.214

GnomAD4 exome

AF:

0.222

AC:

200283

AN:

901983

Hom.:

15964

Cov.:

AF XY:

0.235

AC XY:

61776

AN XY:

263049

show subpopulations

Gnomad4 AFR exome

AF:

0.0632

Gnomad4 AMR exome

AF:

0.0813

Gnomad4 ASJ exome

AF:

0.281

Gnomad4 EAS exome

AF:

0.221

Gnomad4 SAS exome

AF:

0.324

Gnomad4 FIN exome

AF:

0.210

Gnomad4 NFE exome

AF:

0.226

Gnomad4 OTH exome

AF:

0.219

GnomAD4 genome

AF:

0.170

AC:

18892

AN:

110862

Hom.:

1385

Cov.:

AF XY:

0.165

AC XY:

5467

AN XY:

33134

show subpopulations

Gnomad4 AFR

AF:

0.0619

Gnomad4 AMR

AF:

0.112

Gnomad4 ASJ

AF:

0.275

Gnomad4 EAS

AF:

0.228

Gnomad4 SAS

AF:

0.321

Gnomad4 FIN

AF:

0.205

Gnomad4 NFE

AF:

0.223

Gnomad4 OTH

AF:

0.177

Alfa

AF:

0.147

Hom.:

1180

Bravo

AF:

0.158

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Ocular albinism, type I

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Aug 10, 2021

- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Nystagmus 6, congenital, X-linked

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Aug 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

7.1

DANN

Benign

0.38

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over