rs2067280
Positions:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_198273.2(LYSMD3):c.255+1892_255+1893del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 151,982 control chromosomes in the GnomAD database, including 2,054 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.16 ( 2054 hom., cov: 29)
Consequence
LYSMD3
NM_198273.2 intron
NM_198273.2 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.842
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LYSMD3 | NM_198273.2 | c.255+1892_255+1893del | intron_variant | ENST00000315948.11 | |||
LYSMD3 | NM_001286812.1 | c.255+1892_255+1893del | intron_variant | ||||
LYSMD3 | XM_047416694.1 | c.255+1892_255+1893del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LYSMD3 | ENST00000315948.11 | c.255+1892_255+1893del | intron_variant | 1 | NM_198273.2 | P1 | |||
LYSMD3 | ENST00000500869.6 | c.255+1892_255+1893del | intron_variant | 1 | |||||
LYSMD3 | ENST00000509384.5 | c.255+1892_255+1893del | intron_variant | 1 | |||||
LYSMD3 | ENST00000453259.2 | c.255+1892_255+1893del | intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.157 AC: 23879AN: 151864Hom.: 2050 Cov.: 29
GnomAD3 genomes
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29
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.157 AC: 23905AN: 151982Hom.: 2054 Cov.: 29 AF XY: 0.163 AC XY: 12087AN XY: 74256
GnomAD4 genome
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23905
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151982
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29
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12087
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74256
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Asia WGS
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975
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3460
ClinVar
Not reported inComputational scores
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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