3-196306945-T-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_152773.5(DYNLT2B):āc.315A>Gā(p.Val105Val) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000411 in 1,461,258 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 (ā ).
Frequency
Consequence
NM_152773.5 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DYNLT2B | NM_152773.5 | c.315A>G | p.Val105Val | splice_region_variant, synonymous_variant | Exon 3 of 5 | ENST00000325318.10 | NP_689986.2 | |
DYNLT2B | NM_001351628.2 | c.315A>G | p.Val105Val | splice_region_variant, synonymous_variant | Exon 3 of 5 | NP_001338557.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DYNLT2B | ENST00000325318.10 | c.315A>G | p.Val105Val | splice_region_variant, synonymous_variant | Exon 3 of 5 | 1 | NM_152773.5 | ENSP00000324323.5 | ||
ENSG00000272741 | ENST00000431391.1 | n.315A>G | splice_region_variant, non_coding_transcript_exon_variant | Exon 3 of 6 | 5 | ENSP00000405181.1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251316Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135844
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461258Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 726978
GnomAD4 genome Cov.: 31
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