rs4752
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_000583.4(GC):āc.897T>Cā(p.Cys299=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0227 in 1,613,362 control chromosomes in the GnomAD database, including 2,966 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 0.083 ( 1293 hom., cov: 33)
Exomes š: 0.016 ( 1673 hom. )
Consequence
GC
NM_000583.4 synonymous
NM_000583.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.307
Genes affected
GC (HGNC:4187): (GC vitamin D binding protein) The protein encoded by this gene belongs to the albumin gene family. It is a multifunctional protein found in plasma, ascitic fluid, cerebrospinal fluid and on the surface of many cell types. It binds to vitamin D and its plasma metabolites and transports them to target tissues. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Feb 2011]
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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=-0.54).
BP7
?
Synonymous conserved (PhyloP=0.307 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GC | NM_000583.4 | c.897T>C | p.Cys299= | synonymous_variant | 8/13 | ENST00000273951.13 | |
GC | NM_001204307.1 | c.954T>C | p.Cys318= | synonymous_variant | 9/14 | ||
GC | NM_001204306.1 | c.897T>C | p.Cys299= | synonymous_variant | 9/14 | ||
GC | XM_006714177.3 | c.897T>C | p.Cys299= | synonymous_variant | 8/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GC | ENST00000273951.13 | c.897T>C | p.Cys299= | synonymous_variant | 8/13 | 1 | NM_000583.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0830 AC: 12614AN: 152054Hom.: 1290 Cov.: 33
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GnomAD3 exomes AF: 0.0384 AC: 9643AN: 251256Hom.: 656 AF XY: 0.0317 AC XY: 4310AN XY: 135788
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GnomAD4 exome AF: 0.0164 AC: 23938AN: 1461190Hom.: 1673 Cov.: 31 AF XY: 0.0152 AC XY: 11021AN XY: 726948
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GnomAD4 genome ? AF: 0.0830 AC: 12636AN: 152172Hom.: 1293 Cov.: 33 AF XY: 0.0838 AC XY: 6230AN XY: 74386
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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