chr4-71763422-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6_Very_StrongBP7
The NM_000583.4(GC):c.687G>A(p.Lys229=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00128 in 1,584,002 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0013 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0013 ( 3 hom. )
Consequence
GC
NM_000583.4 synonymous
NM_000583.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0530
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.29).
BP6
?
Variant 4-71763422-C-T is Benign according to our data. Variant chr4-71763422-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 773155.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.053 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GC | NM_000583.4 | c.687G>A | p.Lys229= | synonymous_variant | 6/13 | ENST00000273951.13 | |
GC | NM_001204307.1 | c.744G>A | p.Lys248= | synonymous_variant | 7/14 | ||
GC | NM_001204306.1 | c.687G>A | p.Lys229= | synonymous_variant | 7/14 | ||
GC | XM_006714177.3 | c.687G>A | p.Lys229= | synonymous_variant | 6/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GC | ENST00000273951.13 | c.687G>A | p.Lys229= | synonymous_variant | 6/13 | 1 | NM_000583.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00129 AC: 197AN: 152174Hom.: 1 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
197
AN:
152174
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00145 AC: 362AN: 250292Hom.: 1 AF XY: 0.00121 AC XY: 163AN XY: 135252
GnomAD3 exomes
AF:
AC:
362
AN:
250292
Hom.:
AF XY:
AC XY:
163
AN XY:
135252
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00127 AC: 1823AN: 1431710Hom.: 3 Cov.: 26 AF XY: 0.00125 AC XY: 891AN XY: 714134
GnomAD4 exome
AF:
AC:
1823
AN:
1431710
Hom.:
Cov.:
26
AF XY:
AC XY:
891
AN XY:
714134
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00129 AC: 197AN: 152292Hom.: 1 Cov.: 32 AF XY: 0.00122 AC XY: 91AN XY: 74456
GnomAD4 genome
?
AF:
AC:
197
AN:
152292
Hom.:
Cov.:
32
AF XY:
AC XY:
91
AN XY:
74456
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1
AN:
3474
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2022 | GC: BP4, BP7 - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 01, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at