chr3-133775570-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The NM_001063.4(TF):c.1825C>T(p.Arg609Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,614,038 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. R609R) has been classified as Likely benign.
Frequency
Consequence
NM_001063.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TF | NM_001063.4 | c.1825C>T | p.Arg609Trp | missense_variant | 15/17 | ENST00000402696.9 | |
TF | NM_001354703.2 | c.1693C>T | p.Arg565Trp | missense_variant | 21/23 | ||
TF | NM_001354704.2 | c.1444C>T | p.Arg482Trp | missense_variant | 14/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TF | ENST00000402696.9 | c.1825C>T | p.Arg609Trp | missense_variant | 15/17 | 1 | NM_001063.4 | P1 | |
TF | ENST00000467842.1 | n.2819C>T | non_coding_transcript_exon_variant | 1/2 | 1 | ||||
TF | ENST00000461695.1 | c.*125C>T | 3_prime_UTR_variant, NMD_transcript_variant | 5/7 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152152Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461886Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727246
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74318
ClinVar
Submissions by phenotype
Atransferrinemia Pathogenic:1
Likely pathogenic, no assertion criteria provided | clinical testing | Dept of Medicine and Surgery, University of Milano-Bicocca | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at