6-30922706-G-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_020442.6(VARS2):c.2038G>T(p.Val680Leu) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.334 in 1,611,656 control chromosomes in the GnomAD database, including 93,509 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_020442.6 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VARS2 | NM_020442.6 | c.2038G>T | p.Val680Leu | missense_variant, splice_region_variant | Exon 22 of 30 | ENST00000676266.1 | NP_065175.4 | |
VARS2 | NM_001167734.2 | c.2128G>T | p.Val710Leu | missense_variant, splice_region_variant | Exon 22 of 30 | NP_001161206.1 | ||
VARS2 | NM_001167733.3 | c.1618G>T | p.Val540Leu | missense_variant, splice_region_variant | Exon 21 of 29 | NP_001161205.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.280 AC: 42592AN: 152058Hom.: 6847 Cov.: 33
GnomAD3 exomes AF: 0.316 AC: 77549AN: 245306Hom.: 13108 AF XY: 0.324 AC XY: 43282AN XY: 133718
GnomAD4 exome AF: 0.339 AC: 495350AN: 1459482Hom.: 86665 Cov.: 52 AF XY: 0.339 AC XY: 246296AN XY: 726010
GnomAD4 genome AF: 0.280 AC: 42601AN: 152174Hom.: 6844 Cov.: 33 AF XY: 0.281 AC XY: 20908AN XY: 74384
ClinVar
Submissions by phenotype
not specified Benign:2
This variant is classified as Benign based on local population frequency. This variant was detected in 51% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy, Progressive Myoclonus Epilepsy and Abnormal Movements and Neurodegeneration with brain iron accumulation. Number of patients: 47. Only high quality variants are reported. -
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
not provided Benign:2
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Combined oxidative phosphorylation defect type 20 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at