NM_000275.3:c.647_807del

Variant names:

• chr15-28018396-CCTGCTGTGGCCGCCGCCACCTGGAGCCCAAAGCGTCAGCCTGGGTCAGCTCCACCACGATGTGCTCTTCCCTCCCAGGACGACTCGGCCCACTGGCCACTAGGGCCCCTGCCAGGTCCACCTGCAGCAGCGTGGAGTCCACGTGGCTGCTAAGGTTCACGG-C
• rs1555375711
• NM_000275.3:c.647_807del

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 1P and 0B. PP5

The NM_000275.3(OCA2):​c.647_807del variant causes a exon loss, splice region change. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Genomes: not found (cov: 33)
• Consequence: OCA2 NM_000275.3 exon_loss, splice_region
• Clinical Significance: Pathogenic no assertion criteria provided P:3
• Conservation: PhyloP100: 6.48
• Publications: 1 publications found

Genes affected

OCA2 (HGNC:8101): (OCA2 melanosomal transmembrane protein) This gene encodes the human homolog of the mouse p (pink-eyed dilution) gene. The encoded protein is believed to be an integral membrane protein involved in small molecule transport, specifically tyrosine, which is a precursor to melanin synthesis. It is involved in mammalian pigmentation, where it may control skin color variation and act as a determinant of brown or blue eye color. Mutations in this gene result in type 2 oculocutaneous albinism. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

OCA2 Gene-Disease associations (from GenCC):

• oculocutaneous albinism type 2

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, Ambry Genetics, G2P, ClinGen

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PP5: Variant 15-28018396-CCTGCTGTGGCCGCCGCCACCTGGAGCCCAAAGCGTCAGCCTGGGTCAGCTCCACCACGATGTGCTCTTCCCTCCCAGGACGACTCGGCCCACTGGCCACTAGGGCCCCTGCCAGGTCCACCTGCAGCAGCGTGGAGTCCACGTGGCTGCTAAGGTTCACGG-C is Pathogenic according to our data. Variant chr15-28018396-CCTGCTGTGGCCGCCGCCACCTGGAGCCCAAAGCGTCAGCCTGGGTCAGCTCCACCACGATGTGCTCTTCCCTCCCAGGACGACTCGGCCCACTGGCCACTAGGGCCCCTGCCAGGTCCACCTGCAGCAGCGTGGAGTCCACGTGGCTGCTAAGGTTCACGG-C is described in ClinVar as Pathogenic. ClinVar VariationId is 952.Status of the report is no_assertion_criteria_provided, 0 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000275.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OCA2	NM_000275.3	MANE Select	c.647_807del		exon_loss splice_region	Exon 7 of 24	NP_000266.2
	OCA2	NM_001300984.2		c.647_807del		exon_loss splice_region	Exon 7 of 23	NP_001287913.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OCA2	ENST00000354638.8	TSL:1 MANE Select	c.647_807del		exon_loss splice_region	Exon 7 of 24	ENSP00000346659.3
	OCA2	ENST00000353809.9	TSL:1	c.647_807del		exon_loss splice_region	Exon 7 of 23	ENSP00000261276.8
	OCA2	ENST00000431101.1	TSL:3	c.647_*15del		exon_loss splice_region	Exon 7 of 7	ENSP00000415431.1

Frequencies

GnomAD3 genomes Cov.: 33

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:3

Revision: no assertion criteria provided

Submissions by phenotype

Tyrosinase-positive oculocutaneous albinism Pathogenic:2

Sep 26, 2019

Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

Jan 01, 2007

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

Brown oculocutaneous albinism Pathogenic:1

Jan 01, 2007

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		6.5
Mutation Taster		=3/197	disease causing (ClinVar)

Splicing

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

Other links and lift over

dbSNP: rs1555375711; hg19: chr15-28263542;