chr9-12692252-T-G

Variant names:

• chr9-12692252-T-G
• rs2733836
• ENST00000473763.1:c.-85-1660T>G

Variant summary

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

The ENST00000473763.1(TYRP1):​c.-85-1660T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 152,102 control chromosomes in the GnomAD database, including 16,709 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 0.42 (16709 hom., cov: 32)
• Consequence: TYRP1 ENST00000473763.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 3 publications found

Genes affected

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]

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TYRP1	ENST00000473763.1	c.-85-1660T>G		intron_variant	Intron 1 of 1	4		ENSP00000419006.1
LURAP1L-AS1	ENST00000803542.1	n.310-60645A>C		intron_variant	Intron 3 of 3
LURAP1L-AS1	ENST00000803543.1	n.436-3702A>C		intron_variant	Intron 2 of 2
LURAP1L-AS1	ENST00000803544.1	n.100-3702A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64319 AN: 151984 Hom.: 16708 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.0199

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.423 AC: 64332 AN: 152102 Hom.: 16709 Cov.: 32 AF XY: 0.415 AC XY: 30823 AN XY: 74352

African (AFR) AF: 0.175 AC: 7248 AN: 41520

American (AMR) AF: 0.399 AC: 6089 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1665 AN: 3470

East Asian (EAS) AF: 0.0197 AC: 102 AN: 5176

South Asian (SAS) AF: 0.194 AC: 937 AN: 4824

European-Finnish (FIN) AF: 0.588 AC: 6210 AN: 10556

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.598 AC: 40635 AN: 67972

Other (OTH) AF: 0.427 AC: 900 AN: 2106

Alfa AF: 0.512 Hom.: 2729

Bravo AF: 0.402

Asia WGS AF: 0.130 AC: 454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.1
DANN	Benign	0.40
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs2733836; hg19: chr9-12692252;