chr8-96273389-T-C
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_014754.3(PTDSS1):c.270T>C(p.Asn90=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00201 in 1,603,590 control chromosomes in the GnomAD database, including 63 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_014754.3 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTDSS1 | NM_014754.3 | c.270T>C | p.Asn90= | splice_region_variant, synonymous_variant | 2/13 | ENST00000517309.6 | |
LOC105375652 | XR_928431.3 | n.91-7052A>G | intron_variant, non_coding_transcript_variant | ||||
PTDSS1 | NM_001290225.2 | c.2T>C | p.Met1? | start_lost, splice_region_variant | 2/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTDSS1 | ENST00000517309.6 | c.270T>C | p.Asn90= | splice_region_variant, synonymous_variant | 2/13 | 1 | NM_014754.3 | P1 | |
PTDSS1 | ENST00000337004.8 | c.270T>C | p.Asn90= | splice_region_variant, synonymous_variant, NMD_transcript_variant | 2/11 | 1 | |||
PTDSS1 | ENST00000517557.5 | n.344T>C | splice_region_variant, non_coding_transcript_exon_variant | 2/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0110 AC: 1673AN: 152222Hom.: 31 Cov.: 32
GnomAD3 exomes AF: 0.00292 AC: 718AN: 245522Hom.: 14 AF XY: 0.00227 AC XY: 301AN XY: 132596
GnomAD4 exome AF: 0.00107 AC: 1555AN: 1451250Hom.: 32 Cov.: 28 AF XY: 0.000933 AC XY: 674AN XY: 722276
GnomAD4 genome ? AF: 0.0110 AC: 1675AN: 152340Hom.: 31 Cov.: 32 AF XY: 0.0105 AC XY: 779AN XY: 74498
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 28, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at