5-33951588-C-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_016180.5(SLC45A2):āc.1122G>Cā(p.Leu374Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 1,613,970 control chromosomes in the GnomAD database, including 626,996 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_016180.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC45A2 | NM_016180.5 | c.1122G>C | p.Leu374Phe | missense_variant | Exon 5 of 7 | ENST00000296589.9 | NP_057264.4 | |
SLC45A2 | NM_001012509.4 | c.1122G>C | p.Leu374Phe | missense_variant | Exon 5 of 6 | NP_001012527.2 | ||
SLC45A2 | XM_047417259.1 | c.882G>C | p.Leu294Phe | missense_variant | Exon 5 of 7 | XP_047273215.1 | ||
SLC45A2 | NM_001297417.4 | c.*64G>C | 3_prime_UTR_variant | Exon 4 of 4 | NP_001284346.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC45A2 | ENST00000296589.9 | c.1122G>C | p.Leu374Phe | missense_variant | Exon 5 of 7 | 1 | NM_016180.5 | ENSP00000296589.4 | ||
SLC45A2 | ENST00000382102.7 | c.1122G>C | p.Leu374Phe | missense_variant | Exon 5 of 6 | 1 | ENSP00000371534.3 | |||
SLC45A2 | ENST00000509381 | c.*64G>C | 3_prime_UTR_variant | Exon 4 of 4 | 1 | ENSP00000421100.1 | ||||
SLC45A2 | ENST00000510600.1 | c.597G>C | p.Leu199Phe | missense_variant | Exon 4 of 5 | 3 | ENSP00000424010.1 |
Frequencies
GnomAD3 genomes AF: 0.638 AC: 97057AN: 152040Hom.: 42249 Cov.: 32
GnomAD3 exomes AF: 0.645 AC: 162176AN: 251420Hom.: 71927 AF XY: 0.645 AC XY: 87606AN XY: 135888
GnomAD4 exome AF: 0.844 AC: 1233469AN: 1461812Hom.: 584751 Cov.: 48 AF XY: 0.825 AC XY: 599788AN XY: 727216
GnomAD4 genome AF: 0.638 AC: 97039AN: 152158Hom.: 42245 Cov.: 32 AF XY: 0.623 AC XY: 46392AN XY: 74410
ClinVar
Submissions by phenotype
not provided Benign:3
This variant is associated with the following publications: (PMID: 15714523, 24616518, 23071798, 19578363, 18650849, 19384953, 18563784, 22464347, 23660638, 19916045, 17999355) -
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not specified Benign:1
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Oculocutaneous albinism type 4 Benign:1
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Oculocutaneous albinism type 4;C2673584:SKIN/HAIR/EYE PIGMENTATION 5, BLACK/NONBLACK HAIR Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at