chrX-9760704-G-C

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000273.3(GPR143):c.360+13C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0829 in 975,278 control chromosomes in the GnomAD database, including 2,722 homozygotes. There are 22,440 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.088 ( 382 hom., 2592 hem., cov: 22)

Exomes 𝑓: 0.082 ( 2340 hom. 19848 hem. )

Consequence

GPR143
NM_000273.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4O:1

Conservation

PhyloP100: 0.174

Publications

3 publications found

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 Gene-Disease associations (from GenCC):

inherited retinal dystrophy
Inheritance: XL Classification: DEFINITIVE Submitted by: ClinGen
ocular albinism
Inheritance: XL Classification: DEFINITIVE Submitted by: G2P
nystagmus 6, congenital, X-linked
Inheritance: XL Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
X-linked recessive ocular albinism
Inheritance: XL Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)

GPR143 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant X-9760704-G-C is Benign according to our data. Variant chrX-9760704-G-C is described in ClinVar as Benign. ClinVar VariationId is 98629.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
GPR143	NM_000273.3 link	c.360+13C>G	intron_variant	Intron 2 of 8	ENST00000467482.6	NP_000264.2	P51810
GPR143	NM_001440781.1 link	c.360+13C>G	intron_variant	Intron 2 of 8		NP_001427710.1
GPR143	XM_024452388.2 link	c.108+13C>G	intron_variant	Intron 2 of 8		XP_024308156.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
GPR143	ENST00000467482.6 link	c.360+13C>G	intron_variant	Intron 2 of 8	1	NM_000273.3	ENSP00000417161.1	P51810
GPR143	ENST00000447366.5 link	c.108+13C>G	intron_variant	Intron 2 of 7	3		ENSP00000390546.2	H7BZN6
GPR143	ENST00000431126.1 link	c.108+13C>G	intron_variant	Intron 2 of 5	3		ENSP00000406138.1	C9J9N1

Frequencies

GnomAD3 genomes

AF:

0.0884

AC:

9778

AN:

110653

Hom.:

383

Cov.:

show subpopulations

Gnomad AFR

AF:

0.113

Gnomad AMI

AF:

0.0162

Gnomad AMR

AF:

0.0637

Gnomad ASJ

AF:

0.132

Gnomad EAS

AF:

0.0398

Gnomad SAS

AF:

0.0322

Gnomad FIN

AF:

0.0685

Gnomad MID

AF:

0.0979

Gnomad NFE

AF:

0.0857

Gnomad OTH

AF:

0.100

GnomAD2 exomes

AF:

0.0740

AC:

11500

AN:

155426

AF XY:

0.0695

show subpopulations

Gnomad AFR exome

AF:

0.123

Gnomad AMR exome

AF:

0.0447

Gnomad ASJ exome

AF:

0.136

Gnomad EAS exome

AF:

0.0366

Gnomad FIN exome

AF:

0.0757

Gnomad NFE exome

AF:

0.0866

Gnomad OTH exome

AF:

0.0869

GnomAD4 exome

AF:

0.0823

AC:

71122

AN:

864572

Hom.:

2340

Cov.:

AF XY:

0.0810

AC XY:

19848

AN XY:

245168

show subpopulations

African (AFR)

AF:

0.118

AC:

2612

AN:

22149

American (AMR)

AF:

0.0502

AC:

1656

AN:

32988

Ashkenazi Jewish (ASJ)

AF:

0.133

AC:

2347

AN:

17645

East Asian (EAS)

AF:

0.0333

AC:

962

AN:

28911

South Asian (SAS)

AF:

0.0298

AC:

1407

AN:

47202

European-Finnish (FIN)

AF:

0.0763

AC:

3015

AN:

39526

Middle Eastern (MID)

AF:

0.0815

AC:

283

AN:

3473

European-Non Finnish (NFE)

AF:

0.0876

AC:

55566

AN:

634325

Other (OTH)

AF:

0.0854

AC:

3274

AN:

38353

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

2330

4660

6990

9320

11650

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1882

3764

5646

7528

9410

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0883

AC:

9771

AN:

110706

Hom.:

382

Cov.:

AF XY:

0.0786

AC XY:

2592

AN XY:

32958

show subpopulations

African (AFR)

AF:

0.113

AC:

3429

AN:

30423

American (AMR)

AF:

0.0635

AC:

652

AN:

10263

Ashkenazi Jewish (ASJ)

AF:

0.132

AC:

349

AN:

2634

East Asian (EAS)

AF:

0.0399

AC:

142

AN:

3561

South Asian (SAS)

AF:

0.0319

AC:

AN:

2601

European-Finnish (FIN)

AF:

0.0685

AC:

405

AN:

5912

Middle Eastern (MID)

AF:

0.0935

AC:

AN:

214

European-Non Finnish (NFE)

AF:

0.0856

AC:

4532

AN:

52916

Other (OTH)

AF:

0.0985

AC:

148

AN:

1502

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

342

683

1025

1366

1708

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

200

300

400

500

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0564

Hom.:

423

Bravo

AF:

0.0921

ClinVar

Significance: Benign

Submissions summary: Benign:4Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3Other:1

Sep 21, 2019

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Retina International

Significance:not provided

Review Status:no classification provided

Collection Method:literature only

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.41

(source)

DANN

Benign

0.33

PhyloP100

0.17

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over