chr2-75671975-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_003203.5(GCFC2):c.1931A>G(p.Glu644Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00115 in 1,594,876 control chromosomes in the GnomAD database, including 35 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00099 ( 2 hom., cov: 32)
Exomes 𝑓: 0.0012 ( 33 hom. )
Consequence
GCFC2
NM_003203.5 missense
NM_003203.5 missense
Scores
1
5
12
Clinical Significance
Conservation
PhyloP100: 5.30
Genes affected
GCFC2 (HGNC:1317): (GC-rich sequence DNA-binding factor 2) The first mRNA transcript isolated for this gene was part of an artificial chimera derived from two distinct gene transcripts and a primer used in the cloning process (see Genbank accession M29204). A positively charged amino terminus present only in the chimera was determined to bind GC-rich DNA, thus mistakenly thought to identify a transcription factor gene. [provided by RefSeq, Jul 2008]
MRPL19 (HGNC:14052): (mitochondrial ribosomal protein L19) Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S subunit. They have an estimated 75% protein to rRNA composition compared to prokaryotic ribosomes, where this ratio is reversed. Another difference between mammalian mitoribosomes and prokaryotic ribosomes is that the latter contain a 5S rRNA. Among different species, the proteins comprising the mitoribosome differ greatly in sequence, and sometimes in biochemical properties, which prevents easy recognition by sequence homology. This gene encodes a 39S subunit protein. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.01029864).
BP6
?
Variant 2-75671975-T-C is Benign according to our data. Variant chr2-75671975-T-C is described in ClinVar as [Benign]. Clinvar id is 713045.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000993 (151/152110) while in subpopulation EAS AF= 0.028 (145/5178). AF 95% confidence interval is 0.0243. There are 2 homozygotes in gnomad4. There are 81 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GCFC2 | NM_003203.5 | c.1931A>G | p.Glu644Gly | missense_variant | 14/17 | ENST00000321027.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GCFC2 | ENST00000321027.8 | c.1931A>G | p.Glu644Gly | missense_variant | 14/17 | 1 | NM_003203.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000987 AC: 150AN: 151992Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.00212 AC: 533AN: 251270Hom.: 5 AF XY: 0.00184 AC XY: 250AN XY: 135800
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GnomAD4 exome AF: 0.00117 AC: 1686AN: 1442766Hom.: 33 Cov.: 24 AF XY: 0.00110 AC XY: 789AN XY: 718964
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GnomAD4 genome ? AF: 0.000993 AC: 151AN: 152110Hom.: 2 Cov.: 32 AF XY: 0.00109 AC XY: 81AN XY: 74366
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 29, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Pathogenic
DEOGEN2
Benign
T;.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;.
MutationTaster
Benign
D;D;D
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D;D
REVEL
Benign
Sift
Uncertain
D;D;D
Sift4G
Benign
T;T;T
Polyphen
D;.;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
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