rs35415

chr5-33972426-A-Cchr5-33972426-A-Gchr5-33972426-A-T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.82

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]

(HGNC:):

ACMG classification

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	UniProt
SLC45A2	NM_016180.5	c.563-8410T>G		intron_variant		ENST00000296589.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC45A2	ENST00000296589.9	c.563-8410T>G		intron_variant		1	NM_016180.5	P1
	ENST00000504847.1	n.943A>C		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83725 AN: 151870 Hom.: 23642 Cov.: 32

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.: 0 AF XY: 0.507 AC XY: 50880 AN XY: 100400

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.: 32 AF XY: 0.546 AC XY: 40568 AN XY: 74302

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

Other links and lift over

dbSNP: rs35415; hg19: chr5-33972531; COSMIC: COSV56875780;