rs3817672
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001128148.3(TFRC):c.424G>A(p.Gly142Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 1,611,674 control chromosomes in the GnomAD database, including 220,542 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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_001128148.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TFRC | NM_001128148.3 | c.424G>A | p.Gly142Ser | missense_variant | 4/19 | ENST00000360110.9 | |
TFRC | NM_003234.4 | c.424G>A | p.Gly142Ser | missense_variant | 4/19 | ||
TFRC | NM_001313965.2 | c.181G>A | p.Gly61Ser | missense_variant | 3/18 | ||
TFRC | NM_001313966.2 | c.-412-1788G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TFRC | ENST00000360110.9 | c.424G>A | p.Gly142Ser | missense_variant | 4/19 | 1 | NM_001128148.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.425 AC: 64547AN: 151876Hom.: 15433 Cov.: 31
GnomAD3 exomes AF: 0.449 AC: 112205AN: 249668Hom.: 27642 AF XY: 0.458 AC XY: 61748AN XY: 134948
GnomAD4 exome AF: 0.522 AC: 761562AN: 1459680Hom.: 205106 Cov.: 43 AF XY: 0.520 AC XY: 377245AN XY: 726008
GnomAD4 genome ? AF: 0.425 AC: 64554AN: 151994Hom.: 15436 Cov.: 31 AF XY: 0.421 AC XY: 31284AN XY: 74298
ClinVar
Submissions by phenotype
TFRC-related combined immunodeficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 10, 2021 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Nov 12, 2023 | This variant is classified as Benign based on local population frequency. This variant was detected in 59% of patients studied by a panel of primary immunodeficiencies. Number of patients: 57. Only high quality variants are reported. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at