chr11-61341502-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_015533.4(TKFC):c.553G>A(p.Ala185Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.957 in 1,555,306 control chromosomes in the GnomAD database, including 722,710 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 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_015533.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TKFC | NM_015533.4 | c.553G>A | p.Ala185Thr | missense_variant | 6/18 | ENST00000394900.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TKFC | ENST00000394900.8 | c.553G>A | p.Ala185Thr | missense_variant | 6/18 | 1 | NM_015533.4 | P1 | |
TKFC | ENST00000529479.5 | c.550G>A | p.Ala184Thr | missense_variant | 4/16 | 1 | |||
DDB1 | ENST00000540166.5 | c.-166+866C>T | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.840 AC: 127770AN: 152070Hom.: 57536 Cov.: 33
GnomAD3 exomes AF: 0.938 AC: 152342AN: 162394Hom.: 72744 AF XY: 0.942 AC XY: 80664AN XY: 85626
GnomAD4 exome AF: 0.970 AC: 1360701AN: 1403118Hom.: 665180 Cov.: 58 AF XY: 0.968 AC XY: 670564AN XY: 692450
GnomAD4 genome AF: 0.840 AC: 127786AN: 152188Hom.: 57530 Cov.: 33 AF XY: 0.842 AC XY: 62614AN XY: 74406
ClinVar
Submissions by phenotype
Triokinase and FMN cyclase deficiency syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 30, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at