rs55672062
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_014485.3(HPGDS):c.226+13T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00235 in 1,515,976 control chromosomes in the GnomAD database, including 68 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.011 ( 34 hom., cov: 32)
Exomes 𝑓: 0.0013 ( 34 hom. )
Consequence
HPGDS
NM_014485.3 intron
NM_014485.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.861
Genes affected
HPGDS (HGNC:17890): (hematopoietic prostaglandin D synthase) Prostaglandin-D synthase is a sigma class glutathione-S-transferase family member. The enzyme catalyzes the conversion of PGH2 to PGD2 and plays a role in the production of prostanoids in the immune system and mast cells. The presence of this enzyme can be used to identify the differentiation stage of human megakaryocytes. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0115 (1746/152344) while in subpopulation AFR AF= 0.0395 (1642/41580). AF 95% confidence interval is 0.0379. There are 34 homozygotes in gnomad4. There are 832 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 34 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HPGDS | NM_014485.3 | c.226+13T>C | intron_variant | ENST00000295256.10 | |||
HPGDS | XM_005262932.4 | c.134-9117T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HPGDS | ENST00000295256.10 | c.226+13T>C | intron_variant | 1 | NM_014485.3 | P1 | |||
ENST00000667612.1 | n.2375A>G | non_coding_transcript_exon_variant | 1/2 | ||||||
HPGDS | ENST00000514774.1 | n.306+13T>C | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0114 AC: 1742AN: 152226Hom.: 34 Cov.: 32
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GnomAD3 exomes AF: 0.00335 AC: 830AN: 248030Hom.: 14 AF XY: 0.00227 AC XY: 304AN XY: 134018
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GnomAD4 exome AF: 0.00133 AC: 1813AN: 1363632Hom.: 34 Cov.: 22 AF XY: 0.00122 AC XY: 836AN XY: 683906
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GnomAD4 genome ? AF: 0.0115 AC: 1746AN: 152344Hom.: 34 Cov.: 32 AF XY: 0.0112 AC XY: 832AN XY: 74486
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ClinVar
Not reported inComputational scores
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Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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