chr7-74515510-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_005685.4(GTF2IRD1):c.335G>A(p.Arg112His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000769 in 1,612,698 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R112C) has been classified as Likely benign.
Frequency
Consequence
NM_005685.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GTF2IRD1 | NM_005685.4 | c.335G>A | p.Arg112His | missense_variant | 4/27 | ENST00000424337.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GTF2IRD1 | ENST00000424337.7 | c.335G>A | p.Arg112His | missense_variant | 4/27 | 1 | NM_005685.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249902Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135192
GnomAD4 exome AF: 0.0000787 AC: 115AN: 1460524Hom.: 0 Cov.: 32 AF XY: 0.0000743 AC XY: 54AN XY: 726532
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 14, 2023 | The c.431G>A (p.R144H) alteration is located in exon 4 (coding exon 3) of the GTF2IRD1 gene. This alteration results from a G to A substitution at nucleotide position 431, causing the arginine (R) at amino acid position 144 to be replaced by a histidine (H). 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