9-136978985-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000954.6(PTGDS):c.115-8C>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 0.00543 in 1,604,724 control chromosomes in the GnomAD database, including 422 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_000954.6 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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTGDS | NM_000954.6 | c.115-8C>T | splice_region_variant, intron_variant | ENST00000371625.8 | NP_000945.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTGDS | ENST00000371625.8 | c.115-8C>T | splice_region_variant, intron_variant | 1 | NM_000954.6 | ENSP00000360687.3 | ||||
ENSG00000284341 | ENST00000471521.5 | n.115-8C>T | splice_region_variant, intron_variant | 5 | ENSP00000435033.1 |
Frequencies
GnomAD3 genomes AF: 0.0288 AC: 4369AN: 151514Hom.: 225 Cov.: 33
GnomAD3 exomes AF: 0.00741 AC: 1733AN: 233732Hom.: 64 AF XY: 0.00544 AC XY: 697AN XY: 128204
GnomAD4 exome AF: 0.00298 AC: 4337AN: 1453088Hom.: 197 Cov.: 32 AF XY: 0.00252 AC XY: 1821AN XY: 722878
GnomAD4 genome AF: 0.0289 AC: 4376AN: 151636Hom.: 225 Cov.: 33 AF XY: 0.0284 AC XY: 2102AN XY: 74064
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 29, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at