chr4-36290365-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001170700.3(DTHD1):c.888-8C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000261 in 1,532,986 control chromosomes in the GnomAD database, including 1 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 Likely benign (★).
Frequency
Consequence
NM_001170700.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DTHD1 | NM_001170700.3 | c.888-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000639862.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DTHD1 | ENST00000639862.2 | c.888-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_001170700.3 | P2 | |||
DTHD1 | ENST00000456874.3 | c.513-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | A2 | ||||
DTHD1 | ENST00000507598.5 | c.633-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | A2 | ||||
DTHD1 | ENST00000357504.7 | c.18-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152066Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000137 AC: 2AN: 145798Hom.: 0 AF XY: 0.0000259 AC XY: 2AN XY: 77218
GnomAD4 exome AF: 0.0000282 AC: 39AN: 1380920Hom.: 1 Cov.: 29 AF XY: 0.0000235 AC XY: 16AN XY: 679502
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152066Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74276
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 01, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at