Genetic Variant SLC45A2:c.*206T>C (chr5-33951446-A-G) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001297417.4(SLC45A2):c.*206T>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 0.0293 in 1,602,262 control chromosomes in the GnomAD database, including 3,570 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.058 ( 596 hom., cov: 32)

Exomes 𝑓: 0.026 ( 2974 hom. )

Consequence

SLC45A2
NM_001297417.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.21

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 5-33951446-A-G is Benign according to our data. Variant chr5-33951446-A-G is described in ClinVar as [Benign]. Clinvar id is 1222285.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
SLC45A2	NM_016180.5 link	c.1156+108T>C	intron_variant	Intron 5 of 6	ENST00000296589.9	NP_057264.4	Q9UMX9-1A0A076YGN1A0A076YIB8
SLC45A2	NM_001297417.4 link	c.*206T>C	3_prime_UTR_variant	Exon 4 of 4		NP_001284346.2	Q9UMX9D6RGY6
SLC45A2	NM_001012509.4 link	c.1156+108T>C	intron_variant	Intron 5 of 5		NP_001012527.2	Q9UMX9-4
SLC45A2	XM_047417259.1 link	c.916+108T>C	intron_variant	Intron 5 of 6		XP_047273215.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SLC45A2	ENST00000509381 link	c.*206T>C	3_prime_UTR_variant	Exon 4 of 4	1		ENSP00000421100.1	D6RGY6
SLC45A2	ENST00000296589.9 link	c.1156+108T>C	intron_variant	Intron 5 of 6	1	NM_016180.5	ENSP00000296589.4	Q9UMX9-1
SLC45A2	ENST00000382102.7 link	c.1156+108T>C	intron_variant	Intron 5 of 5	1		ENSP00000371534.3	Q9UMX9-4
SLC45A2	ENST00000510600.1 link	c.631+108T>C	intron_variant	Intron 4 of 4	3		ENSP00000424010.1	D6RBP8

Frequencies

GnomAD3 genomes

AF:

0.0577

AC:

8782

AN:

152140

Hom.:

594

Cov.:

show subpopulations

Gnomad AFR

AF:

0.129

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0474

Gnomad ASJ

AF:

0.0173

Gnomad EAS

AF:

0.268

Gnomad SAS

AF:

0.155

Gnomad FIN

AF:

0.000753

Gnomad MID

AF:

0.0924

Gnomad NFE

AF:

0.00539

Gnomad OTH

AF:

0.0642

GnomAD3 exomes

AF:

0.0588

AC:

14017

AN:

238380

Hom.:

1138

AF XY:

0.0604

AC XY:

7872

AN XY:

130274

show subpopulations

Gnomad AFR exome

AF:

0.137

Gnomad AMR exome

AF:

0.0448

Gnomad ASJ exome

AF:

0.0181

Gnomad EAS exome

AF:

0.267

Gnomad SAS exome

AF:

0.145

Gnomad FIN exome

AF:

0.000556

Gnomad NFE exome

AF:

0.00734

Gnomad OTH exome

AF:

0.0419

GnomAD4 exome

AF:

0.0263

AC:

38164

AN:

1450000

Hom.:

2974

Cov.:

AF XY:

0.0299

AC XY:

21547

AN XY:

721524

show subpopulations

Gnomad4 AFR exome

AF:

0.136

Gnomad4 AMR exome

AF:

0.0456

Gnomad4 ASJ exome

AF:

0.0169

Gnomad4 EAS exome

AF:

0.255

Gnomad4 SAS exome

AF:

0.148

Gnomad4 FIN exome

AF:

0.000781

Gnomad4 NFE exome

AF:

0.00477

Gnomad4 OTH exome

AF:

0.0446

GnomAD4 genome

AF:

0.0578

AC:

8797

AN:

152262

Hom.:

596

Cov.:

AF XY:

0.0600

AC XY:

4464

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.129

Gnomad4 AMR

AF:

0.0475

Gnomad4 ASJ

AF:

0.0173

Gnomad4 EAS

AF:

0.268

Gnomad4 SAS

AF:

0.155

Gnomad4 FIN

AF:

0.000753

Gnomad4 NFE

AF:

0.00538

Gnomad4 OTH

AF:

0.0634

Alfa

AF:

0.0194

Hom.:

124

Bravo

AF:

0.0632

Asia WGS

AF:

0.164

AC:

570

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

May 16, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

DANN

Benign

0.80

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over