rs2382360

Variant names:

• chr9-12710413-T-C
• rs2382360
• ENST00000417638.1:n.273-9787A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000417638.1(LURAP1L-AS1):​n.273-9787A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 151,298 control chromosomes in the GnomAD database, including 2,071 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.16 (2071 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: LURAP1L-AS1 ENST00000417638.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 0 publications found

Genes affected

LURAP1L-AS1 (HGNC:49761): (LURAP1L antisense RNA 1)

TYRP1 (HGNC:12450): (tyrosinase related protein 1) This gene encodes a melanosomal enzyme that belongs to the tyrosinase family and plays an important role in the melanin biosynthetic pathway. Defects in this gene are the cause of rufous oculocutaneous albinism and oculocutaneous albinism type III. [provided by RefSeq, Mar 2009]

TYRP1 Gene-Disease associations (from GenCC):

• oculocutaneous albinism type 3

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LURAP1L-AS1	NR_125775.1	n.317-9787A>G		intron_variant	Intron 3 of 3
TYRP1	NM_000550.3	c.*1231T>C		downstream_gene_variant		ENST00000388918.10	NP_000541.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TYRP1	ENST00000388918.10	c.*1231T>C		downstream_gene_variant		1	NM_000550.3	ENSP00000373570.4

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23772 AN: 151176 Hom.: 2075 Cov.: 31

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.0931

Gnomad MID AF: 0.262

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.157 AC: 23778 AN: 151298 Hom.: 2071 Cov.: 31 AF XY: 0.154 AC XY: 11412 AN XY: 73910

African (AFR) AF: 0.216 AC: 8932 AN: 41396

American (AMR) AF: 0.162 AC: 2444 AN: 15106

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 679 AN: 3460

East Asian (EAS) AF: 0.127 AC: 647 AN: 5114

South Asian (SAS) AF: 0.181 AC: 871 AN: 4806

European-Finnish (FIN) AF: 0.0931 AC: 983 AN: 10558

Middle Eastern (MID) AF: 0.268 AC: 74 AN: 276

European-Non Finnish (NFE) AF: 0.127 AC: 8602 AN: 67568

Other (OTH) AF: 0.187 AC: 393 AN: 2102

Alfa AF: 0.144 Hom.: 373

Bravo AF: 0.163

Asia WGS AF: 0.170 AC: 585 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.47
DANN	Benign	0.48
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2382360; hg19: chr9-12710413; COSMIC: COSV66358424;