2-196773130-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_012086.5(GTF3C3):c.1855G>A(p.Val619Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000747 in 1,605,668 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_012086.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GTF3C3 | ENST00000263956.8 | c.1855G>A | p.Val619Ile | missense_variant | Exon 14 of 18 | 1 | NM_012086.5 | ENSP00000263956.3 | ||
GTF3C3 | ENST00000416690.5 | c.202G>A | p.Val68Ile | missense_variant | Exon 4 of 4 | 3 | ENSP00000391724.1 | |||
GTF3C3 | ENST00000651042.1 | n.*187G>A | non_coding_transcript_exon_variant | Exon 15 of 19 | ENSP00000499170.1 | |||||
GTF3C3 | ENST00000651042.1 | n.*187G>A | 3_prime_UTR_variant | Exon 15 of 19 | ENSP00000499170.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000813 AC: 2AN: 245992Hom.: 0 AF XY: 0.0000151 AC XY: 2AN XY: 132816
GnomAD4 exome AF: 0.00000550 AC: 8AN: 1453478Hom.: 0 Cov.: 28 AF XY: 0.00000691 AC XY: 5AN XY: 723164
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1855G>A (p.V619I) alteration is located in exon 14 (coding exon 14) of the GTF3C3 gene. This alteration results from a G to A substitution at nucleotide position 1855, causing the valine (V) at amino acid position 619 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at