rs3818110
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_182961.4(SYNE1):c.25458+24C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 1,610,822 control chromosomes in the GnomAD database, including 128,689 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_182961.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYNE1 | ENST00000367255.10 | c.25458+24C>T | intron_variant | Intron 140 of 145 | 1 | NM_182961.4 | ENSP00000356224.5 | |||
SYNE1 | ENST00000354674.5 | c.1992+24C>T | intron_variant | Intron 12 of 17 | 5 | NM_001347702.2 | ENSP00000346701.4 |
Frequencies
GnomAD3 genomes AF: 0.429 AC: 64863AN: 151290Hom.: 14403 Cov.: 31
GnomAD3 exomes AF: 0.408 AC: 101697AN: 249532Hom.: 21530 AF XY: 0.404 AC XY: 54569AN XY: 134996
GnomAD4 exome AF: 0.392 AC: 571844AN: 1459412Hom.: 114285 Cov.: 35 AF XY: 0.393 AC XY: 285575AN XY: 726014
GnomAD4 genome AF: 0.429 AC: 64914AN: 151410Hom.: 14404 Cov.: 31 AF XY: 0.425 AC XY: 31449AN XY: 74000
ClinVar
Submissions by phenotype
not specified Benign:1
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not provided Benign:1
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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at