3-196291381-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_152773.5(DYNLT2B):c.382-7T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000298 in 1,609,564 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_152773.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DYNLT2B | ENST00000325318.10 | c.382-7T>C | splice_region_variant, intron_variant | Intron 4 of 4 | 1 | NM_152773.5 | ENSP00000324323.5 | |||
ENSG00000272741 | ENST00000431391.1 | n.317+15562T>C | intron_variant | Intron 3 of 5 | 5 | ENSP00000405181.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152238Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000203 AC: 5AN: 245704Hom.: 0 AF XY: 0.0000225 AC XY: 3AN XY: 133110
GnomAD4 exome AF: 0.0000302 AC: 44AN: 1457326Hom.: 0 Cov.: 30 AF XY: 0.0000372 AC XY: 27AN XY: 724946
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152238Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74378
ClinVar
Submissions by phenotype
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at