5-33947384-G-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_016180.5(SLC45A2):c.1157-10C>A variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000931 in 1,611,832 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000096 ( 0 hom. )
Consequence
SLC45A2
NM_016180.5 splice_polypyrimidine_tract, intron
NM_016180.5 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.002214
2
Clinical Significance
Conservation
PhyloP100: 0.981
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 Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
?
Variant 5-33947384-G-T is Benign according to our data. Variant chr5-33947384-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 2994662.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC45A2 | NM_016180.5 | c.1157-10C>A | splice_polypyrimidine_tract_variant, intron_variant | ENST00000296589.9 | |||
SLC45A2 | NM_001012509.4 | c.1157-10C>A | splice_polypyrimidine_tract_variant, intron_variant | ||||
SLC45A2 | XM_047417259.1 | c.917-10C>A | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC45A2 | ENST00000296589.9 | c.1157-10C>A | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_016180.5 | P1 | |||
SLC45A2 | ENST00000382102.7 | c.1157-10C>A | splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
SLC45A2 | ENST00000510600.1 | c.632-10C>A | splice_polypyrimidine_tract_variant, intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152226Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.00000959 AC: 14AN: 1459606Hom.: 0 Cov.: 30 AF XY: 0.00000688 AC XY: 5AN XY: 726382
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 21, 2023 | - - |
Computational scores
Source:
Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at