5-33946038-A-G

Variant summary

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

The NM_001012509.4(SLC45A2):​c.*1110T>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 0.0273 in 985,366 control chromosomes in the GnomAD database, including 2,107 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 0.066 ( 1221 hom., cov: 33)
Exomes 𝑓: 0.020 ( 886 hom. )

Consequence

SLC45A2
NM_001012509.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.398
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]

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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=-0.85).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC45A2NM_016180.5 linkc.1368+1125T>C intron_variant Intron 6 of 6 ENST00000296589.9 NP_057264.4 Q9UMX9-1A0A076YGN1A0A076YIB8
SLC45A2NM_001012509.4 linkc.*1110T>C 3_prime_UTR_variant Exon 6 of 6 NP_001012527.2 Q9UMX9-4
SLC45A2XM_047417259.1 linkc.1128+1125T>C intron_variant Intron 6 of 6 XP_047273215.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC45A2ENST00000382102 linkc.*1110T>C 3_prime_UTR_variant Exon 6 of 6 1 ENSP00000371534.3 Q9UMX9-4
SLC45A2ENST00000296589.9 linkc.1368+1125T>C intron_variant Intron 6 of 6 1 NM_016180.5 ENSP00000296589.4 Q9UMX9-1

Frequencies

GnomAD3 genomes
AF:
0.0657
AC:
9992
AN:
152166
Hom.:
1212
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0330
Gnomad AMI
AF:
0.00987
Gnomad AMR
AF:
0.242
Gnomad ASJ
AF:
0.0308
Gnomad EAS
AF:
0.429
Gnomad SAS
AF:
0.197
Gnomad FIN
AF:
0.0134
Gnomad MID
AF:
0.114
Gnomad NFE
AF:
0.0185
Gnomad OTH
AF:
0.0969
GnomAD4 exome
AF:
0.0202
AC:
16845
AN:
833082
Hom.:
886
Cov.:
28
AF XY:
0.0201
AC XY:
7715
AN XY:
384706
show subpopulations
Gnomad4 AFR exome
AF:
0.0281
Gnomad4 AMR exome
AF:
0.297
Gnomad4 ASJ exome
AF:
0.0320
Gnomad4 EAS exome
AF:
0.426
Gnomad4 SAS exome
AF:
0.189
Gnomad4 FIN exome
AF:
0.00362
Gnomad4 NFE exome
AF:
0.0124
Gnomad4 OTH exome
AF:
0.0573
GnomAD4 genome
AF:
0.0657
AC:
10012
AN:
152284
Hom.:
1221
Cov.:
33
AF XY:
0.0731
AC XY:
5447
AN XY:
74474
show subpopulations
Gnomad4 AFR
AF:
0.0330
Gnomad4 AMR
AF:
0.243
Gnomad4 ASJ
AF:
0.0308
Gnomad4 EAS
AF:
0.429
Gnomad4 SAS
AF:
0.197
Gnomad4 FIN
AF:
0.0134
Gnomad4 NFE
AF:
0.0185
Gnomad4 OTH
AF:
0.0964
Alfa
AF:
0.0381
Hom.:
433
Bravo
AF:
0.0851
Asia WGS
AF:
0.244
AC:
847
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
1.6
DANN
Benign
0.57

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.

Other links and lift over

dbSNP: rs35406; hg19: chr5-33946143; API