9-5908647-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005511.2(MLANA):āc.296A>Gā(p.Asn99Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000246 in 1,614,054 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_005511.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MLANA | NM_005511.2 | c.296A>G | p.Asn99Ser | missense_variant | 5/5 | ENST00000381477.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MLANA | ENST00000381477.8 | c.296A>G | p.Asn99Ser | missense_variant | 5/5 | 1 | NM_005511.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000256 AC: 39AN: 152160Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000318 AC: 80AN: 251412Hom.: 0 AF XY: 0.000265 AC XY: 36AN XY: 135868
GnomAD4 exome AF: 0.000245 AC: 358AN: 1461776Hom.: 0 Cov.: 30 AF XY: 0.000256 AC XY: 186AN XY: 727184
GnomAD4 genome AF: 0.000256 AC: 39AN: 152278Hom.: 0 Cov.: 33 AF XY: 0.000201 AC XY: 15AN XY: 74456
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 05, 2024 | The c.296A>G (p.N99S) alteration is located in exon 5 (coding exon 4) of the MLANA gene. This alteration results from a A to G substitution at nucleotide position 296, causing the asparagine (N) at amino acid position 99 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at