rs1049817
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_001035521.3(GTF3C2):āc.2346T>Cā(p.Pro782=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 1,609,112 control chromosomes in the GnomAD database, including 139,582 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 0.47 ( 18591 hom., cov: 32)
Exomes š: 0.40 ( 120991 hom. )
Consequence
GTF3C2
NM_001035521.3 synonymous
NM_001035521.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.246
Genes affected
GTF3C2 (HGNC:4665): (general transcription factor IIIC subunit 2) Contributes to DNA binding activity. Involved in transcription by RNA polymerase III. Located in nucleoplasm. Part of transcription factor TFIIIC complex. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.59).
BP7
?
Synonymous conserved (PhyloP=-0.246 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GTF3C2 | NM_001035521.3 | c.2346T>C | p.Pro782= | synonymous_variant | 17/19 | ENST00000264720.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GTF3C2 | ENST00000264720.8 | c.2346T>C | p.Pro782= | synonymous_variant | 17/19 | 1 | NM_001035521.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.472 AC: 71710AN: 151934Hom.: 18532 Cov.: 32
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GnomAD3 exomes AF: 0.419 AC: 104001AN: 248488Hom.: 23762 AF XY: 0.407 AC XY: 54753AN XY: 134464
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GnomAD4 exome AF: 0.400 AC: 582118AN: 1457060Hom.: 120991 Cov.: 31 AF XY: 0.397 AC XY: 287919AN XY: 725090
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GnomAD4 genome ? AF: 0.472 AC: 71840AN: 152052Hom.: 18591 Cov.: 32 AF XY: 0.471 AC XY: 35016AN XY: 74318
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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
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at