17-82037555-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_016286.4(DCXR):c.53-8C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00481 in 1,544,190 control chromosomes in the GnomAD database, including 348 homozygotes. 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 Benign (★★).
Frequency
Consequence
NM_016286.4 splice_region, intron
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 |
---|---|---|---|---|---|---|---|---|
DCXR | NM_016286.4 | c.53-8C>T | splice_region_variant, intron_variant | Intron 1 of 7 | ENST00000306869.7 | NP_057370.1 | ||
DCXR | NM_001195218.1 | c.53-14C>T | intron_variant | Intron 1 of 7 | NP_001182147.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0257 AC: 3908AN: 152216Hom.: 198 Cov.: 34
GnomAD3 exomes AF: 0.00531 AC: 750AN: 141280Hom.: 35 AF XY: 0.00396 AC XY: 308AN XY: 77874
GnomAD4 exome AF: 0.00252 AC: 3509AN: 1391860Hom.: 150 Cov.: 32 AF XY: 0.00218 AC XY: 1498AN XY: 687948
GnomAD4 genome AF: 0.0257 AC: 3915AN: 152330Hom.: 198 Cov.: 34 AF XY: 0.0245 AC XY: 1828AN XY: 74494
ClinVar
Submissions by phenotype
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at