ENST00000382102.7:c.*682T>C

Variant names:

• chr5-33946466-A-G
• rs35407
• ENST00000382102.7:c.*682T>C

Variant summary

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

The ENST00000382102.7(SLC45A2):​c.*682T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.908 in 985,534 control chromosomes in the GnomAD database, including 425,705 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 0.72 (45957 hom., cov: 33)
  • Exomes 𝑓: 0.94 (379748 hom.)
• Consequence: SLC45A2 ENST00000382102.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.393
• Publications: 26 publications found

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 Gene-Disease associations (from GenCC):

• oculocutaneous albinism type 4

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, Ambry Genetics, G2P

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000382102.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC45A2	NM_016180.5	MANE Select	c.1368+697T>C		intron	N/A	NP_057264.4
	SLC45A2	NM_001012509.4		c.*682T>C		3_prime_UTR	Exon 6 of 6	NP_001012527.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC45A2	ENST00000382102.7	TSL:1	c.*682T>C		3_prime_UTR	Exon 6 of 6	ENSP00000371534.3
	SLC45A2	ENST00000296589.9	TSL:1 MANE Select	c.1368+697T>C		intron	N/A	ENSP00000296589.4

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109163 AN: 152120 Hom.: 45943 Cov.: 33

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.935

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.969

Gnomad OTH AF: 0.695

GnomAD4 exome AF: 0.942 AC: 785300 AN: 833296 Hom.: 379748 Cov.: 41 AF XY: 0.942 AC XY: 362503 AN XY: 384804

African (AFR) AF: 0.330 AC: 5213 AN: 15784

American (AMR) AF: 0.545 AC: 541 AN: 992

Ashkenazi Jewish (ASJ) AF: 0.935 AC: 4819 AN: 5152

East Asian (EAS) AF: 0.117 AC: 426 AN: 3630

South Asian (SAS) AF: 0.252 AC: 4142 AN: 16466

European-Finnish (FIN) AF: 0.996 AC: 277 AN: 278

Middle Eastern (MID) AF: 0.563 AC: 912 AN: 1620

European-Non Finnish (NFE) AF: 0.980 AC: 746466 AN: 762074

Other (OTH) AF: 0.824 AC: 22504 AN: 27300

GnomAD4 genome AF: 0.717 AC: 109206 AN: 152238 Hom.: 45957 Cov.: 33 AF XY: 0.704 AC XY: 52403 AN XY: 74446

African (AFR) AF: 0.385 AC: 15975 AN: 41500

American (AMR) AF: 0.600 AC: 9180 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.935 AC: 3248 AN: 3472

East Asian (EAS) AF: 0.125 AC: 647 AN: 5182

South Asian (SAS) AF: 0.247 AC: 1193 AN: 4824

European-Finnish (FIN) AF: 0.985 AC: 10461 AN: 10622

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.969 AC: 65943 AN: 68022

Other (OTH) AF: 0.694 AC: 1468 AN: 2114

Alfa AF: 0.841 Hom.: 124753

Bravo AF: 0.676

Asia WGS AF: 0.263 AC: 919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.53
PhyloP100		-0.39
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: rs35407; hg19: chr5-33946571;