NM_005264.8:c.792dupT
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_005264.8(GFRA1):c.792dupT(p.Thr265TyrfsTer20) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 1,596,794 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_005264.8 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000290 AC: 4AN: 137918Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249688Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 134990
GnomAD4 exome AF: 0.0000117 AC: 17AN: 1458876Hom.: 0 Cov.: 30 AF XY: 0.00000964 AC XY: 7AN XY: 725948
GnomAD4 genome AF: 0.0000290 AC: 4AN: 137918Hom.: 0 Cov.: 32 AF XY: 0.0000295 AC XY: 2AN XY: 67780
ClinVar
Submissions by phenotype
GFRA1-related disorder Pathogenic:1
The GFRA1 c.792dupT variant is predicted to result in a frameshift and premature protein termination (p.Thr265Tyrfs*20). To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0042% of alleles in individuals of African descent in gnomAD. Frameshift variants in GFRA1 are expected to be pathogenic. This variant is interpreted as likely pathogenic. -
not provided Pathogenic:1
Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Has not been previously published as pathogenic or benign to our knowledge -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at