chr10-116089842-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005264.8(GFRA1):c.1096A>G(p.Thr366Ala) variant causes a missense change. The variant allele was found at a frequency of 0.0936 in 1,613,376 control chromosomes in the GnomAD database, including 7,578 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_005264.8 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GFRA1 | NM_005264.8 | c.1096A>G | p.Thr366Ala | missense_variant | 9/11 | ENST00000355422.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GFRA1 | ENST00000355422.11 | c.1096A>G | p.Thr366Ala | missense_variant | 9/11 | 5 | NM_005264.8 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0941 AC: 14309AN: 152040Hom.: 703 Cov.: 32
GnomAD3 exomes AF: 0.104 AC: 26244AN: 251218Hom.: 1516 AF XY: 0.104 AC XY: 14157AN XY: 135784
GnomAD4 exome AF: 0.0935 AC: 136671AN: 1461216Hom.: 6874 Cov.: 33 AF XY: 0.0950 AC XY: 69038AN XY: 726944
GnomAD4 genome ? AF: 0.0941 AC: 14318AN: 152160Hom.: 704 Cov.: 32 AF XY: 0.0956 AC XY: 7112AN XY: 74388
ClinVar
Submissions by phenotype
GFRA1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 21, 2019 | This variant is classified as 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