Variant rs35415 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_016180.5(SLC45A2):c.563-8410T>G variant causes a intron change. The variant allele was found at a frequency of 0.54 in 332,740 control chromosomes in the GnomAD database, including 51,206 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 0.55 ( 23646 hom., cov: 32)

Exomes 𝑓: 0.53 ( 27560 hom. )

Consequence

SLC45A2
NM_016180.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.82

Variant links:

Genes affected

SLC45A2 (HGNC:16472): (solute carrier family 45 member 2) This gene encodes a transporter protein that mediates melanin synthesis. The protein is expressed in a high percentage of melanoma cell lines. Mutations in this gene are a cause of oculocutaneous albinism type 4, and polymorphisms in this gene are associated with variations in skin and hair color. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2009]

SLC45A2 links:

ENSG00000250914 (HGNC:):

ENSG00000250914 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.58).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC45A2	NM_016180.5 linkuse as main transcript	c.563-8410T>G		intron_variant		ENST00000296589.9	NP_057264.4	Q9UMX9-1A0A076YGN1A0A076YIB8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC45A2	ENST00000296589.9 linkuse as main transcript	c.563-8410T>G		intron_variant		1	NM_016180.5	ENSP00000296589.4		Q9UMX9-1

Frequencies

GnomAD3 genomes

AF:

0.551

AC:

83725

AN:

151870

Hom.:

23642

Cov.:

show subpopulations

Gnomad AFR

AF:

0.529

Gnomad AMI

AF:

0.586

Gnomad AMR

AF:

0.477

Gnomad ASJ

AF:

0.583

Gnomad EAS

AF:

0.447

Gnomad SAS

AF:

0.210

Gnomad FIN

AF:

0.662

Gnomad MID

AF:

0.364

Gnomad NFE

AF:

0.596

Gnomad OTH

AF:

0.519

GnomAD4 exome

AF:

0.531

AC:

95980

AN:

180750

Hom.:

27560

Cov.:

AF XY:

0.507

AC XY:

50880

AN XY:

100400

show subpopulations

Gnomad4 AFR exome

AF:

0.543

Gnomad4 AMR exome

AF:

0.426

Gnomad4 ASJ exome

AF:

0.559

Gnomad4 EAS exome

AF:

0.459

Gnomad4 SAS exome

AF:

0.222

Gnomad4 FIN exome

AF:

0.663

Gnomad4 NFE exome

AF:

0.601

Gnomad4 OTH exome

AF:

0.568

GnomAD4 genome

AF:

0.551

AC:

83749

AN:

151990

Hom.:

23646

Cov.:

AF XY:

0.546

AC XY:

40568

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.529

Gnomad4 AMR

AF:

0.476

Gnomad4 ASJ

AF:

0.583

Gnomad4 EAS

AF:

0.447

Gnomad4 SAS

AF:

0.210

Gnomad4 FIN

AF:

0.662

Gnomad4 NFE

AF:

0.596

Gnomad4 OTH

AF:

0.515

Alfa

AF:

0.569

Hom.:

15275

Bravo

AF:

0.543

Asia WGS

AF:

0.322

AC:

1125

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

3.3

DANN

Benign

0.66

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

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over