chr9-5909152-T-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005511.2(MLANA):c.*444T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 159,332 control chromosomes in the GnomAD database, including 30,680 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 0.60 ( 28915 hom., cov: 32)
Exomes 𝑓: 0.68 ( 1765 hom. )
Consequence
MLANA
NM_005511.2 3_prime_UTR
NM_005511.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.302
Genes affected
MLANA (HGNC:7124): (melan-A) Located in endoplasmic reticulum membrane; melanosome; and trans-Golgi network. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.78).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MLANA | NM_005511.2 | c.*444T>G | 3_prime_UTR_variant | 5/5 | ENST00000381477.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MLANA | ENST00000381477.8 | c.*444T>G | 3_prime_UTR_variant | 5/5 | 1 | NM_005511.2 | P1 | ||
KIAA2026 | ENST00000436015.6 | c.*230+1463A>C | intron_variant, NMD_transcript_variant | 3 | |||||
KIAA2026 | ENST00000443149.2 | n.96+1463A>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.605 AC: 91916AN: 151910Hom.: 28917 Cov.: 32
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GnomAD4 exome AF: 0.682 AC: 4984AN: 7304Hom.: 1765 Cov.: 0 AF XY: 0.683 AC XY: 2679AN XY: 3922
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GnomAD4 genome ? AF: 0.605 AC: 91940AN: 152028Hom.: 28915 Cov.: 32 AF XY: 0.599 AC XY: 44475AN XY: 74288
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at