chrX-9748675-C-T

Variant names:

• chrX-9748675-C-T
• rs376437604
• NM_000273.3:c.456-9G>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2 BP4_Strong BP6_Moderate

The NM_000273.3(GPR143):​c.456-9G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000891 in 112,258 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0000089 (0 hom., 0 hem., cov: 23)
  • Exomes 𝑓: 0.0 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: GPR143 NM_000273.3 intron
• Scores: Splicing: ADA: 0.0005339
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.576
• Publications: 0 publications found

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)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant X-9748675-C-T is Benign according to our data. Variant chrX-9748675-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 1541754.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPR143	NM_000273.3	c.456-9G>A		intron_variant	Intron 3 of 8	ENST00000467482.6	NP_000264.2
GPR143	NM_001440781.1	c.456-9G>A		intron_variant	Intron 3 of 8		NP_001427710.1
GPR143	XM_024452388.2	c.204-9G>A		intron_variant	Intron 3 of 8		XP_024308156.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPR143	ENST00000467482.6	c.456-9G>A		intron_variant	Intron 3 of 8	1	NM_000273.3	ENSP00000417161.1
GPR143	ENST00000447366.5	c.204-9G>A		intron_variant	Intron 3 of 7	3		ENSP00000390546.2
GPR143	ENST00000431126.1	c.204-9G>A		intron_variant	Intron 3 of 5	3		ENSP00000406138.1
GPR143	ENST00000480178.1	n.64-9G>A		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.00000891 AC: 1 AN: 112258 Hom.: 0 Cov.: 23

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000370

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1030273 Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0 AN XY: 304217

African (AFR) AF: 0.00 AC: 0 AN: 25224

American (AMR) AF: 0.00 AC: 0 AN: 34837

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18901

East Asian (EAS) AF: 0.00 AC: 0 AN: 29921

South Asian (SAS) AF: 0.00 AC: 0 AN: 51943

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40141

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3936

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 781500

Other (OTH) AF: 0.00 AC: 0 AN: 43870

GnomAD4 genome AF: 0.00000891 AC: 1 AN: 112258 Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0 AN XY: 34422

African (AFR) AF: 0.00 AC: 0 AN: 30899

American (AMR) AF: 0.00 AC: 0 AN: 10654

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2657

East Asian (EAS) AF: 0.00 AC: 0 AN: 3552

South Asian (SAS) AF: 0.000370 AC: 1 AN: 2703

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6165

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 239

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 53194

Other (OTH) AF: 0.00 AC: 0 AN: 1509

Alfa AF: 0.00 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Dec 16, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely 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	-0.80
CADD	Benign	11
DANN	Benign	0.72
PhyloP100		-0.58

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.00053
dbscSNV1_RF	Benign	0.038
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

Other links and lift over

dbSNP: rs376437604; hg19: chrX-9716715;