chr8-96273400-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_014754.3(PTDSS1):c.271+10G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000021 in 1,431,330 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
PTDSS1
NM_014754.3 intron
NM_014754.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.00700
Genes affected
PTDSS1 (HGNC:9587): (phosphatidylserine synthase 1) The protein encoded by this gene catalyzes the formation of phosphatidylserine from either phosphatidylcholine or phosphatidylethanolamine. Phosphatidylserine localizes to the mitochondria-associated membrane of the endoplasmic reticulum, where it serves a structural role as well as a signaling role. Defects in this gene are a cause of Lenz-Majewski hyperostotic dwarfism. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2014]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
?
Variant 8-96273400-G-A is Benign according to our data. Variant chr8-96273400-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1958312.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTDSS1 | NM_014754.3 | c.271+10G>A | intron_variant | ENST00000517309.6 | |||
LOC105375652 | XR_928431.3 | n.91-7063C>T | intron_variant, non_coding_transcript_variant | ||||
PTDSS1 | NM_001290225.2 | c.3+10G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTDSS1 | ENST00000517309.6 | c.271+10G>A | intron_variant | 1 | NM_014754.3 | P1 | |||
PTDSS1 | ENST00000337004.8 | c.271+10G>A | intron_variant, NMD_transcript_variant | 1 | |||||
PTDSS1 | ENST00000517557.5 | n.345+10G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome AF: 0.00000210 AC: 3AN: 1431330Hom.: 0 Cov.: 26 AF XY: 0.00000140 AC XY: 1AN XY: 713330
GnomAD4 exome
AF:
AC:
3
AN:
1431330
Hom.:
Cov.:
26
AF XY:
AC XY:
1
AN XY:
713330
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 06, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at