rs3746721
Variant names:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_018556.4(SIRPG):c.1140C>T(p.Tyr380Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 1,569,130 control chromosomes in the GnomAD database, including 59,925 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 0.24 ( 5274 hom., cov: 31)
Exomes 𝑓: 0.26 ( 54651 hom. )
Consequence
SIRPG
NM_018556.4 synonymous
NM_018556.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.70
Genes affected
SIRPG (HGNC:15757): (signal regulatory protein gamma) The protein encoded by this gene is a member of the signal-regulatory protein (SIRP) family, and also belongs to the immunoglobulin superfamily. SIRP family members are receptor-type transmembrane glycoproteins known to be involved in the negative regulation of receptor tyrosine kinase-coupled signaling processes. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
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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=-0.98).
BP7
Synonymous conserved (PhyloP=-1.7 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.239 AC: 36364AN: 151846Hom.: 5279 Cov.: 31
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GnomAD3 exomes AF: 0.302 AC: 57237AN: 189316Hom.: 10125 AF XY: 0.313 AC XY: 31388AN XY: 100364
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GnomAD4 exome AF: 0.263 AC: 372430AN: 1417164Hom.: 54651 Cov.: 32 AF XY: 0.270 AC XY: 189025AN XY: 701004
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GnomAD4 genome AF: 0.239 AC: 36369AN: 151966Hom.: 5274 Cov.: 31 AF XY: 0.246 AC XY: 18306AN XY: 74274
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at