NM_006950.3:c.1982+10C>A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_006950.3(SYN1):c.1982+10C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000493 in 1,013,393 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_006950.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYN1 | ENST00000295987.13 | c.1982+10C>A | intron_variant | Intron 12 of 12 | 2 | NM_006950.3 | ENSP00000295987.7 | |||
SYN1 | ENST00000340666.5 | c.1982+10C>A | intron_variant | Intron 12 of 12 | 1 | ENSP00000343206.4 | ||||
SYN1 | ENST00000640721.1 | c.70+696C>A | intron_variant | Intron 1 of 1 | 5 | ENSP00000492857.1 |
Frequencies
GnomAD3 genomes Cov.: 24
GnomAD4 exome AF: 0.00000493 AC: 5AN: 1013393Hom.: 0 Cov.: 31 AF XY: 0.00000930 AC XY: 3AN XY: 322663
GnomAD4 genome Cov.: 24
ClinVar
Submissions by phenotype
Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders Uncertain:1Benign:1
This variant was classified as: Uncertain significance. The available evidence on this variant's pathogenicity is insufficient or conflicting. The following ACMG criteria were applied in classifying this variant: PM2,BP4. -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at