rs6096822
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_080607.3(VSTM2L):c.121+5573A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,106 control chromosomes in the GnomAD database, including 2,471 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 0.14 ( 2471 hom., cov: 32)
Consequence
VSTM2L
NM_080607.3 intron
NM_080607.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.109
Genes affected
VSTM2L (HGNC:16096): (V-set and transmembrane domain containing 2 like) Predicted to enable cell-cell adhesion mediator activity. Involved in negative regulation of neuron apoptotic process. Located in cytoplasm and extracellular region. [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=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VSTM2L | NM_080607.3 | c.121+5573A>G | intron_variant | ENST00000373461.9 | |||
LOC124904896 | XR_007067576.1 | n.3371-2185T>C | intron_variant, non_coding_transcript_variant | ||||
VSTM2L | XM_011528530.2 | c.121+5573A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VSTM2L | ENST00000373461.9 | c.121+5573A>G | intron_variant | 1 | NM_080607.3 | P1 | |||
VSTM2L | ENST00000373459.4 | c.121+5573A>G | intron_variant | 3 | |||||
VSTM2L | ENST00000448944.1 | c.121+5573A>G | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.143 AC: 21762AN: 151986Hom.: 2462 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.143 AC: 21799AN: 152106Hom.: 2471 Cov.: 32 AF XY: 0.142 AC XY: 10558AN XY: 74376
GnomAD4 genome
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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