rs2762462

Variant names:

• chr9-12699776-T-C
• rs2762462
• NM_000550.3:c.913+1121T>C

Your query was ambiguous. Multiple possible variants found:

• chr9-12699776-T-C
• chr9-12699776-T-G

Variant summary

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

The NM_000550.3(TYRP1):​c.913+1121T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.635 in 151,874 control chromosomes in the GnomAD database, including 32,113 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 0.63 (32113 hom., cov: 31)
• Consequence: TYRP1 NM_000550.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.31
• Publications: 7 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TYRP1	NM_000550.3	c.913+1121T>C		intron_variant	Intron 4 of 7	ENST00000388918.10	NP_000541.1
TYRP1	XM_047423841.1	c.709-2495T>C		intron_variant	Intron 3 of 4		XP_047279797.1
LURAP1L-AS1	NR_125775.1	n.*223A>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TYRP1	ENST00000388918.10	c.913+1121T>C		intron_variant	Intron 4 of 7	1	NM_000550.3	ENSP00000373570.4

Frequencies

GnomAD3 genomes AF: 0.635 AC: 96346 AN: 151756 Hom.: 32098 Cov.: 31

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.635 AC: 96397 AN: 151874 Hom.: 32113 Cov.: 31 AF XY: 0.627 AC XY: 46509 AN XY: 74236

African (AFR) AF: 0.540 AC: 22382 AN: 41450

American (AMR) AF: 0.533 AC: 8107 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2125 AN: 3470

East Asian (EAS) AF: 0.131 AC: 672 AN: 5124

South Asian (SAS) AF: 0.511 AC: 2465 AN: 4824

European-Finnish (FIN) AF: 0.741 AC: 7850 AN: 10594

Middle Eastern (MID) AF: 0.630 AC: 184 AN: 292

European-Non Finnish (NFE) AF: 0.747 AC: 50703 AN: 67902

Other (OTH) AF: 0.629 AC: 1324 AN: 2104

Alfa AF: 0.707 Hom.: 39321

Bravo AF: 0.616

Asia WGS AF: 0.309 AC: 1077 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.097
DANN	Benign	0.51
PhyloP100		-3.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs2762462; hg19: chr9-12699776;