rs8070488
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The ENST00000329138.9(HGS):āc.1785T>Cā(p.Pro595=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 1,608,460 control chromosomes in the GnomAD database, including 41,440 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: š 0.25 ( 5303 hom., cov: 33)
Exomes š: 0.22 ( 36137 hom. )
Consequence
HGS
ENST00000329138.9 synonymous
ENST00000329138.9 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -6.42
Genes affected
HGS (HGNC:4897): (hepatocyte growth factor-regulated tyrosine kinase substrate) The protein encoded by this gene regulates endosomal sorting and plays a critical role in the recycling and degradation of membrane receptors. The encoded protein sorts monoubiquitinated membrane proteins into the multivesicular body, targeting these proteins for lysosome-dependent degradation. [provided by RefSeq, Dec 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BP7
Synonymous conserved (PhyloP=-6.41 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HGS | NM_004712.5 | c.1785T>C | p.Pro595= | synonymous_variant | 18/22 | ENST00000329138.9 | NP_004703.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HGS | ENST00000329138.9 | c.1785T>C | p.Pro595= | synonymous_variant | 18/22 | 1 | NM_004712.5 | ENSP00000331201 | P1 |
Frequencies
GnomAD3 genomes AF: 0.253 AC: 38508AN: 151956Hom.: 5280 Cov.: 33
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GnomAD3 exomes AF: 0.208 AC: 51092AN: 245384Hom.: 5745 AF XY: 0.205 AC XY: 27417AN XY: 133640
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GnomAD4 exome AF: 0.219 AC: 318745AN: 1456384Hom.: 36137 Cov.: 34 AF XY: 0.216 AC XY: 156831AN XY: 724578
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GnomAD4 genome AF: 0.254 AC: 38572AN: 152076Hom.: 5303 Cov.: 33 AF XY: 0.250 AC XY: 18559AN XY: 74324
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Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
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RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at