7-74515421-G-C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The ENST00000455841.6(GTF2IRD1):āc.342G>Cā(p.Ser114=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000294 in 1,563,168 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. S114S) has been classified as Likely benign.
Frequency
Consequence
ENST00000455841.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GTF2IRD1 | NM_005685.4 | c.266-20G>C | intron_variant | ENST00000424337.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GTF2IRD1 | ENST00000424337.7 | c.266-20G>C | intron_variant | 1 | NM_005685.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000341 AC: 6AN: 175882Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 94632
GnomAD4 exome AF: 0.0000191 AC: 27AN: 1410984Hom.: 0 Cov.: 32 AF XY: 0.0000115 AC XY: 8AN XY: 698026
GnomAD4 genome AF: 0.000125 AC: 19AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74342
ClinVar
Submissions by phenotype
GTF2IRD1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 18, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at