rs928946
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_153215.3(LSMEM2):c.99G>A(p.Gly33=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00648 in 1,610,978 control chromosomes in the GnomAD database, including 622 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 0.034 ( 312 hom., cov: 33)
Exomes 𝑓: 0.0036 ( 310 hom. )
Consequence
LSMEM2
NM_153215.3 synonymous
NM_153215.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.00
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP7
?
Synonymous conserved (PhyloP=-1 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.117 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LSMEM2 | NM_153215.3 | c.99G>A | p.Gly33= | synonymous_variant | 2/4 | ENST00000316436.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LSMEM2 | ENST00000316436.4 | c.99G>A | p.Gly33= | synonymous_variant | 2/4 | 1 | NM_153215.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0344 AC: 5236AN: 152216Hom.: 312 Cov.: 33
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GnomAD3 exomes AF: 0.00778 AC: 1899AN: 244034Hom.: 108 AF XY: 0.00558 AC XY: 739AN XY: 132466
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GnomAD4 exome AF: 0.00355 AC: 5185AN: 1458644Hom.: 310 Cov.: 33 AF XY: 0.00292 AC XY: 2119AN XY: 725388
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GnomAD4 genome ? AF: 0.0345 AC: 5254AN: 152334Hom.: 312 Cov.: 33 AF XY: 0.0327 AC XY: 2437AN XY: 74496
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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