Variant rs147565972 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_000550.3(TYRP1):c.1409-18dupA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 1,602,834 control chromosomes in the GnomAD database, including 310,593 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.48 ( 21667 hom., cov: 0)

Exomes 𝑓: 0.61 ( 288926 hom. )

Consequence

TYRP1
NM_000550.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.918

Variant links:

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]

TYRP1 links:

TYRP1 (HGNC:):

TYRP1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 9-12708958-T-TA is Benign according to our data. Variant chr9-12708958-T-TA is described in ClinVar as [Benign]. Clinvar id is 256643.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TYRP1	NM_000550.3 linkuse as main transcript	c.1409-18dupA		intron_variant		ENST00000388918.10	NP_000541.1	P17643
LURAP1L-AS1	NR_125775.1 linkuse as main transcript	n.317-8333dupT		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TYRP1	ENST00000388918.10 linkuse as main transcript	c.1409-18dupA		intron_variant		1	NM_000550.3	ENSP00000373570.4		P17643

Frequencies

GnomAD3 genomes

AF:

0.482

AC:

73149

AN:

151718

Hom.:

21667

Cov.:

show subpopulations

Gnomad AFR

AF:

0.205

Gnomad AMI

AF:

0.526

Gnomad AMR

AF:

0.426

Gnomad ASJ

AF:

0.550

Gnomad EAS

AF:

0.0112

Gnomad SAS

AF:

0.233

Gnomad FIN

AF:

0.717

Gnomad MID

AF:

0.446

Gnomad NFE

AF:

0.676

Gnomad OTH

AF:

0.487

GnomAD3 exomes

AF:

0.508

AC:

125401

AN:

246804

Hom.:

38129

AF XY:

0.508

AC XY:

67730

AN XY:

133414

show subpopulations

Gnomad AFR exome

AF:

0.198

Gnomad AMR exome

AF:

0.443

Gnomad ASJ exome

AF:

0.564

Gnomad EAS exome

AF:

0.00825

Gnomad SAS exome

AF:

0.262

Gnomad FIN exome

AF:

0.720

Gnomad NFE exome

AF:

0.675

Gnomad OTH exome

AF:

0.549

GnomAD4 exome

AF:

0.608

AC:

882367

AN:

1450998

Hom.:

288926

Cov.:

AF XY:

0.599

AC XY:

432924

AN XY:

722520

show subpopulations

Gnomad4 AFR exome

AF:

0.188

Gnomad4 AMR exome

AF:

0.441

Gnomad4 ASJ exome

AF:

0.564

Gnomad4 EAS exome

AF:

0.00443

Gnomad4 SAS exome

AF:

0.267

Gnomad4 FIN exome

AF:

0.715

Gnomad4 NFE exome

AF:

0.675

Gnomad4 OTH exome

AF:

0.554

GnomAD4 genome

AF:

0.482

AC:

73152

AN:

151836

Hom.:

21667

Cov.:

AF XY:

0.474

AC XY:

35215

AN XY:

74234

show subpopulations

Gnomad4 AFR

AF:

0.205

Gnomad4 AMR

AF:

0.426

Gnomad4 ASJ

AF:

0.550

Gnomad4 EAS

AF:

0.0111

Gnomad4 SAS

AF:

0.233

Gnomad4 FIN

AF:

0.717

Gnomad4 NFE

AF:

0.676

Gnomad4 OTH

AF:

0.481

Alfa

AF:

0.505

Hom.:

2709

Asia WGS

AF:

0.138

AC:

484

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Oculocutaneous albinism type 3

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Dec 05, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over