rs2209277

Variant names:

• chr9-12706236-T-C
• rs2209277
• NM_000550.3:c.1261+1531T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000550.3(TYRP1):​c.1261+1531T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 151,916 control chromosomes in the GnomAD database, including 22,660 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 0.51 (22660 hom., cov: 32)
• Consequence: TYRP1 NM_000550.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TYRP1	NM_000550.3	c.1261+1531T>C		intron_variant	Intron 6 of 7	ENST00000388918.10	NP_000541.1
LURAP1L-AS1	NR_125775.1	n.317-5610A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TYRP1	ENST00000388918.10	c.1261+1531T>C		intron_variant	Intron 6 of 7	1	NM_000550.3	ENSP00000373570.4

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76847 AN: 151800 Hom.: 22652 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.0202

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.506 AC: 76892 AN: 151916 Hom.: 22660 Cov.: 32 AF XY: 0.498 AC XY: 36986 AN XY: 74248

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.0201

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.718

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.503

Alfa AF: 0.628 Hom.: 39066

Bravo AF: 0.480

Asia WGS AF: 0.155 AC: 542 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.52

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

Publications

LitVar

Other links and lift over

dbSNP: rs2209277; hg19: chr9-12706236;